Recombinant monoclonal antibodies and corresponding antigens for colon and pancreatic cancers

ABSTRACT

The present invention provides for purified or highly pure recombinant monoclonal antibodies that bind to human colorectal and pancreatic carcinoma-associated antigens (CPAA), along with nucleic acid sequences encoding the antibody chains, and the amino acid sequences corresponding to said nucleic acids and uses for said sequences.

RELATED APPLICATION

This application is a divisional of U.S. patent application Ser. No.14/739,701, filed Jun. 15, 2015, which is a divisional of U.S. patentapplication Ser. No. 13/012,679, filed Jan. 24, 2011, now U.S. Pat. No.9,169,326, which is a divisional of U.S. patent application Ser. No.12/825,022, filed Jun. 28, 2010, now U.S. Pat. No. 8,535,667, which is acontinuation of U.S. patent application Ser. No. 12/000,701, filed Dec.17, 2007, now U.S. Pat. No. 7,763,720, which is a divisional of U.S.patent application Ser. No. 11/404,566, filed Apr. 14, 2006, now U.S.Pat. No. 7,314,622, which claims benefit of U.S. Provisional Appl. No.60/671,481, filed Apr. 15, 2005, the disclosures of each of which arehereby incorporated by reference in their entireties.

SEQUENCE DISCLOSURE

This application includes as part of its disclosure a biologicalsequence listing which is being concurrently submitted through EFS-Web.Said biological sequence listing is contained in a file named“43282o1007.txt” which was created Feb. 9, 2017, and has a size of14,795 bytes, and is hereby incorporated by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to the field of recombinant monoclonalantibodies and peptides and their uses in clinical and scientificprocedures, including diagnostic procedures, especially where suchprocesses involve the detection of human colorectal and pancreaticcarcinoma-associated antigens (CPAA), and the characterization of theepitopes recognized by said recombinant monoclonal antibodies andpeptides. The present invention also provides anti-CPAA antibodies andpeptides in the form of diagnostic compounds and/or pharmaceuticalcompositions, useful for the diagnostic and/or therapeutic methods ofthe present invention for diagnosing and/or treating colorectal andpancreatic carcinoma-associated pathologies.

BACKGROUND OF THE INVENTION

According to the most recent data from the World Health Organization,ten million people around the world were diagnosed with the cancer in2000, and six million died from it. Moreover, statistics indicate thatthe cancer incidence rate is on the rise around the globe. In America,for example, projections suggest that forty percent of those alive todaywill be diagnosed with some form of cancer at some point in their lives.By 2010, that number will have climbed to fifty percent. Of all cancers,colorectal cancer is the second leading cause of cancer-related deathsin the U.S., while pancreatic cancer is the eleventh most common cancerand the fourth leading cause of cancer death in both men and women. Thisgrim scenario shows the great need for new cancer diagnostics andtherapies.

Modern technology, such as that involving the use of hybridomas, hasmade available to researchers and clinicians sources of highly specificand potent monoclonal antibodies useful in general diagnostic andclinical procedures. For example, there are now therapeutic antibodiesfor the treatment of cancer, such as HERCEPTIN® (trastuzumab, Genentech)for metastatic breast cancer and PANOREX® (endrecolomab,Centocor/GlaxoSmithKline) approved in Germany for the treatment ofcolorectal cancer.

Yet the most important challenge in fighting cancer, according to Dr.Leland Hartwell, Nobel Laureate and Director of the Fred HutchinsonCancer Research Center, remains the pursuit of early diagnosis. TheEconomist (Oct. 4, 2004). The more advanced a cancer is when diagnosed,the less likely it is that therapy will be effective.

Hence, despite the advances in cancer research, there remains a need,for recombinant monoclonal antibodies useful for the early diagnosis andtreatment of colon and pancreatic carcinomas.

SUMMARY OF THE INVENTION

An object of the present invention provides for recombinant monoclonalantibodies, or portions of recombinant monoclonal antibodies (peptides)having specificity directed to antigens and epitopes of human colorectaland pancreatic carcinoma-associated antigens (CPAA). It is therefore anobject of the present invention to provide for a recombinant monoclonalantibody or a portion thereof having specificity for CPAA proteins andpeptides.

A further object of the present invention provides for oligonucleotides,such as cDNAs, whose nucleotide sequences (genes) encode part or all ofthe heavy and light chains of the aforementioned recombinant antibodies.Accordingly, an aspect of the present invention provides for a geneencoding the variable region of a monoclonal antibody, specificallyrecognizing CPAA, especially determinants or epitopes that commonlyexist in all CPAA.

A further object of the present invention provides for a recombinantvector comprising the above genes. A further object of the presentinvention provides for a transformant obtained using the aboverecombinant vector.

It is a still further object of the present invention to providerecombinant antibodies specific for CPAA, wherein said antibodies aretagged with markers, making them easily isolatable as well as affordingversatility in using said antibodies for research, diagnostic andclinical purposes. A further aspect of the invention provides for achimeric antibody that includes the variable regions of the heavy andlight chains of CPAA-specific murine antibody linked to the humanimmunoglobulin gamma-1 and kappa constant regions, respectively.

It is another object of the present invention to provide a method ofusing the recombinant antibodies disclosed herein for research,diagnostic, and clinical uses. Particularly, an object of the presentinvention provides a diagnostic tool for the early detection of cancers,perhaps in patients without symptoms of disease. Another aspect providesfor an immunohistochemical tool for distinguishing between slow andaggressive pancreatic cancers.

Another object of the invention provides a method for promoting tumorregression or triggering the death of transformed cells comprisingadministering to a patient in need thereof an antibody, portion,fragment, peptide or derivative thereof that binds to a CPAA antigen,wherein a said antibody is administered in sufficient amounts to promotetumor regression or cell death.

Yet another object of the present invention provides for methods havingutility for in vitro, in situ and/or in vivo diagnosis and/or treatmentof animal cells, tissues or pathologies associated with the presence ofCPAA, using anti-CPAA antibodies and/or anti-CPAA peptides. The presentinvention also provides anti-CPAA antibodies and peptides in the form ofpharmaceutical and/or diagnostic compounds and/or compositions, usefulfor the diagnostic and/or therapeutic methods of the present inventionfor diagnosing and/or treating CPAA-related pathologies.

The present invention is also directed to an anti-CPAA chimeric antibodycomprising two light chains and two heavy chains, each of the chainscomprising at least part of a human constant region and at least part ofa variable (V) region of non-human origin having specificity to CPAA,said antibody binding with high affinity and/or high avidity to aninhibiting and/or neutralizing epitope of CPAA-associated cells. Theinvention also includes a fragment or a derivative such an antibody,such as one or more portions of the antibody chain, such as the heavychain constant, joining, diversity or variable regions, or the lightchain constant, joining or variable regions.

It is a further object of the invention to identify the specificepitopes associated with the CPAA peptides identified by the monoclonalantibodies or portions thereof. Such antigenic sequences may be usefulin generating additional antigen-binding ligands, or be used as vaccinesor other immunostimulatory means.

Methods are also provided for making and using anti-CPAA antibodies andpeptides for various utilities of the present invention, such as but notlimited to, hybridoma, recombinant or chemical synthetic methods forproducing anti-CPAA antibodies or anti-CPAA peptides according to thepresent invention; detecting CPAA in a solution or cell; inhibiting oneor more biological activities of CPAA-bearing cells in vitro, in situ orin vivo, including killing such CPAA-bearing cells. Hence, suchinhibition and killing can include treatment methods of the presentinvention for alleviating symptoms or pathologies involving CPAA-bearingcells, such as malignancies.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

FIG. 1 is a tracing showing an HPLC elution profile of the Hollinshead“vaccine”, a partially purified preparation of colorectal and pancreaticcarcinoma cell membranes.

FIG. 2 presents the entire cDNA sequence (SEQ ID NO:1) of the NPC-1kappa light chain.

FIG. 3 depicts the nucleic acid sequence (SEQ ID NO:2) and correspondingamino acid sequence (SEQ ID NO:3) of the NPC-1 kappa light chain.

FIGS. 4A-4B present the entire cDNA sequence (SEQ ID NO:4) of NPC-1heavy chain.

FIGS. 5A-5B depict the nucleic acid sequence (SEQ ID NO:5) andcorresponding amino acid sequence (SEQ ID NO:6) of the NPC-1 heavychain.

FIG. 6 depicts the CDR 1 (SEQ ID NO:7), CDR 2 (SEQ ID NO:8), and CDR 3(SEQ ID NO:9) of NPC-1 in the Light Chain Sequence.

FIG. 7 identifies the CDR 1 (SEQ ID NO:10), CDR 2 (SEQ ID NO:11), andCDR 3 (SEQ IN NO:12) of NPC-1 in the Heavy Chain Sequence.

DETAILED DESCRIPTION OF THE INVENTION

It should be understood that this invention is not limited to theparticular methodology, protocols, and reagents, etc., described hereinand as such may vary. The terminology used herein is for the purpose ofdescribing particular embodiments only, and is not intended to limit thescope of the present invention, which is defined solely by the claims.

As used herein and in the claims, the singular forms “a,” “an,” and“the” include the plural reference unless the context clearly indicatesotherwise. Thus, for example, the reference to an antibody is areference to one or more such antibodies, including equivalents thereofknown to those skilled in the art. Other than in the operating examples,or where otherwise indicated, all numbers expressing quantities ofingredients or reaction conditions used herein should be understood asmodified in all instances by the term “about.” The term “about” whenused in connection with percentages may mean±1%.

All patents and other publications identified are expressly incorporatedherein by reference for the purpose of describing and disclosing, forexample, the methodologies described in such publications that might beused in connection with the present invention. These publications areprovided solely for their disclosure prior to the filing date of thepresent application. Nothing in this regard should be construed as anadmission that the inventors are not entitled to antedate suchdisclosure by virtue of prior invention or for any other reason. Allstatements as to the date or representation as to the contents of thesedocuments is based on the information available to the applicants anddoes not constitute any admission as to the correctness of the dates orcontents of these documents.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as those commonly understood to one of ordinaryskill in the art to which this invention pertains. Although any knownmethods, devices, and materials may be used in the practice or testingof the invention, the methods, devices, and materials in this regard aredescribed here.

The present invention provides for recombinant monoclonal antibodies andpeptides and their uses in clinical and scientific procedures, includingdiagnostic procedures, especially where such processes involve thedetection of human colorectal and pancreatic carcinoma-associatedantigens (CPAA), and the characterization of the epitopes recognized bysaid recombinant monoclonal antibodies and peptides. The presentinvention also provides anti-CPAA antibodies and peptides in the form ofdiagnostic compounds and/or pharmaceutical compositions, useful for thediagnostic and/or therapeutic methods of the present invention fordiagnosing and/or treating colorectal and pancreaticcarcinoma-associated pathologies.

Generally, monoclonal antibodies are used as invaluable reagents indiagnostics. In fact, they have played a major role in deciphering thefunctions of various bio-molecules in cryptic biosynthetic pathways.These have also become the reagents of choice for identification andcharacterization of tumor specific antigens and have become a valuabletool in the classification of cancer.

With the advent of methods of molecular biology and recombinanttechnology, it is now possible to produce antibody molecules byrecombinant means and thereby generate gene sequences that code forspecific amino acid sequences found in the polypeptide structure of theantibodies. Such antibodies can be produced by either cloning the genesequences encoding the polypeptide chains of said antibodies or bydirect synthesis of said polypeptide chains, with assembly of thesynthesized chains to form active tetrameric (H₂ L₂) structures withaffinity for specific epitopes and antigenic determinants. This haspermitted the ready production of antibodies having sequencescharacteristic of neutralizing antibodies from different species andsources.

Regardless of the source of the antibodies, or how they arerecombinantly constructed, or how they are synthesized, in vitro or invivo, using transgenic animals, large cell cultures of laboratory orcommercial size, using transgenic plants, or by direct chemicalsynthesis employing no living organisms at any stage of the process, allantibodies have a similar overall 3 dimensional structure. Thisstructure is often given as H₂ L₂ and refers to the fact that antibodiescommonly comprise two light (L) amino acid chains and 2 heavy (H) aminoacid chains. Both chains have regions capable of interacting with astructurally complementary antigenic target. The regions interactingwith the target are referred to as “variable” or “V” regions and arecharacterized by differences in amino acid sequence from antibodies ofdifferent antigenic specificity. The variable regions of either H or Lchains contain the amino acid sequences capable of specifically bindingto antigenic targets.

As used herein, the term “antigen binding region” refers to that portionof an antibody molecule which contains the amino acid residues thatinteract with an antigen and confer on the antibody its specificity andaffinity for the antigen. The antibody region includes the “framework”amino acid residues necessary to maintain the proper conformation of theantigen-binding residues.

Within the variable regions of the H or L chains that provide for theantigen binding regions are smaller sequences dubbed “hypervariable”because of their extreme variability between antibodies of differingspecificity. Such hypervariable regions are also referred to as“complementarity determining regions” or “CDR” regions. These CDRregions account for the basic specificity of the antibody for aparticular antigenic determinant structure.

The CDRs represent non-contiguous stretches of amino acids within thevariable regions but, regardless of species, the positional locations ofthese critical amino acid sequences within the variable heavy and lightchain regions have been found to have similar locations within the aminoacid sequences of the variable chains. The variable heavy and lightchains of all antibodies each have 3 CDR regions, each non-contiguouswith the others (termed L1, L2, L3, H1, H2, H3) for the respective light(L) and heavy (H) chains. The accepted CDR regions have been describedby Kabat et al, 252 J. Biol. Chem. 6609-16 (1977), and CDR loops may beidentified by applying these rules during an examination of a linearamino acid sequence. The rules for defining the CDR-H3 loop can vary,however (see Chapter 4, Antibody Engineering: Methods & Protocols, (Lo,ed. Humana Press, Totowa, N.J., 2004)), and the actual boundaries ofsome CDR-H3 loops may not be identified without experimental techniquessuch as circular dichroism, nuclear magnetic resonance, or X-raycrystallography.

In all mammalian species, antibody peptides contain constant (i.e.,highly conserved) and variable regions, and, within the latter, thereare the CDRs and the so-called “framework regions” made up of amino acidsequences within the variable region of the heavy or light chain butoutside the CDRs.

Regarding the antigenic determinate recognized by the CDR regions of theantibody, this is also referred to as the “epitope.” In other words,epitope refers to that portion of any molecule capable of beingrecognized by, and bound by, an antibody (the corresponding antibodybinding region may be referred to as a paratope). In general, epitopesconsist of chemically active surface groupings of molecules, forexample, amino acids or sugar side chains, and have specificthree-dimensional structural characteristics as well as specific chargecharacteristics.

An “antigen” is a molecule or a portion of a molecule capable of beingbound by an antibody which is additionally capable of inducing an animalto produce an antibody capable of binding to an epitope of that antigen.An antigen may have one or more than one epitope. The specific reactionreferred to above is meant to indicate that the antigen will react, in ahighly selective manner, with its corresponding antibody and not withthe multitude of other antibodies which may be evoked by other antigens.

Thus, the term “antibody” is meant to include both intact immunoglobulinmolecules as well as portions, fragments, peptides and derivativesthereof, such as, for example, Fab, Fab′, F(ab′)₂, Fv, CDR regions, orany portion or peptide sequence of the antibody that is capable ofbinding antigen or epitope. An antibody is said to be “capable ofbinding” a molecule if it is capable of specifically reacting with themolecule to thereby bind the molecule to the antibody.

Antibody also includes chimeric antibodies, anti-idiotypic (anti-Id)antibodies to antibodies that can be labeled in soluble or bound form,as well as fragments, portions, regions, peptides or derivativesthereof, provided by any known technique, such as, but not limited to,enzymatic cleavage, peptide synthesis, or recombinant techniques. Suchantibodies of the present invention are capable of binding portions ofCPAA or CPAA-bearing cells. Antibody fragments or portions may lack theFc fragment of intact antibody, clear more rapidly from the circulation,and may have less non-specific tissue binding than an intact antibody.Examples of antibody may be produced from intact antibodies usingmethods well known in the art, for example by proteolytic cleavage withenzymes such as papain (to produce Fab fragments) or pepsin (to produceF(ab′)₂ fragments). See e.g., Wahl et al., 24 J. Nucl. Med. 316-25(1983). Portions of antibodies may be made by any of the above methods,or may be made by expressing a portion of the recombinant molecule. Forexample, the CDR region(s) of a recombinant antibody may be isolated andsubcloned into the appropriate expression vector. See, e.g., U.S. Pat.No. 6,680,053.

NPC-1 Oligonucleotide and Amino Acid Sequences

The present invention includes, within its scope, DNA sequences encodingthe variable regions of the light and heavy chains of the anti-CPAAantibody of the present invention. A nucleic acid sequence encoding thevariable region of the light chain of NPC-1 is presented in FIG. 2 (SEQID NO:1). A nucleic acid sequence encoding the variable region of theheavy chain of NPC-1 is presented in FIG. 4 (SEQ ID NO:4).

The present invention includes, within its scope, an amino acid sequenceof the NPC-1 light chain comprising the peptides depicted in FIG. 3 (SEQID NO:3), and an amino acid sequence of the NPC-1 heavy chain comprisingthe peptides of FIG. 5 (SEQ ID NO:6). Further, the present inventionincludes the CDR regions depicted for the kappa light chain in FIG. 6,which include the amino acid sequences for CDR1 (SEQ ID NO:7):SASSSISYMY; CDR2 (SEQ ID NO:8): DTSKLAS; and CDR3 (SEQ ID NO:9):HQRDSYPWT. The invention similarly identifies the CDR regions for theheavy chain in FIG. 7, which include the amino acid sequences for CDR 1(SEQ ID NO:10): SKFGVN (SEQ ID NO:10); CDR 2 (SEQ ID NO:11):VIWGDGSTSYNSGLIS; and CDR3: (SEQ ID NO:12) CVKPGGDY.

Included also within the scope of the invention is any oligonucleotidesequence that encodes the amino acid sequence of NPC-1 or a peptidethereof. Because the genetic code is degenerate, more than one codon canbe used to encode a particular amino acid. Using the genetic code, oneor more different oligonucleotides can be identified, each of whichwould be capable of encoding the amino acid. The probability that aparticular oligonucleotide will, in fact, constitute the actualXXX-encoding sequence can be estimated by considering abnormal basepairing relationships and the frequency with which a particular codon isactually used (to encode a particular amino acid) in eukaryotic orprokaryotic cells expressing an anti-CPAA antibody or portion. Such“codon usage rules” are disclosed by Lathe, et al., 183 J. Molec. Biol.1-12 (1985). Using the “codon usage rules” of Lathe, a singleoligonucleotide, or a set of oligonucleotides, that contains atheoretical “most probable” nucleotide sequence capable of encodinganti-CPAA sequences is identified.

Although occasionally an amino acid sequence can be encoded by only asingle oligonucleotide, frequently the amino acid sequence can beencoded by any of a set of similar oligonucleotides. Importantly,whereas all of the members of this set contain oligonucleotides whichare capable of encoding the peptide fragment and, thus, potentiallycontain the same oligonucleotide sequence as the gene which encodes thepeptide fragment, only one member of the set contains the nucleotidesequence that is identical to the nucleotide sequence of the gene.Because this member is present within the set, and is capable ofhybridizing to DNA even in the presence of the other members of the set,it is possible to employ the unfractionated set of oligonucleotides inthe same manner in which one would employ a single oligonucleotide toclone the gene that encodes the protein.

The oligonucleotide, or set of oligonucleotides, containing thetheoretical “most probable” sequence capable of encoding an anti-CPAAantibody or peptide including a variable or constant region is used toidentify the sequence of a complementary oligonucleotide or set ofoligo-nucleotides which is capable of hybridizing to the “most probable”sequence, or set of sequences. An oligonucleotide containing such acomplementary sequence can be employed as a probe to identify andisolate the variable or constant region anti-CPAA gene (Sambrook et al.,1989).

A suitable oligonucleotide, or set of oligonucleotides, which is capableof encoding a peptide of NPC-1 (or which is complementary to such anoligonucleotide, or set of oligonucleotides) is identified (using theabove-described procedure), synthesized, and hybridized by means wellknown in the art, against a DNA or a cDNA preparation derived from cellswhich are capable of expressing anti-CPAA antibodies or variable orconstant regions thereof. Single stranded oligonucleotide moleculescomplementary to the “most probable” anti-CPAA region peptide codingsequences can be synthesized using procedures which are well known tothose of ordinary skill in the art. See Belagaje et al., 254 J. Biol.Chem. 5765-80 (1979); Maniatis et al., in Molecular Mechanisms in theControl of Gene Expression (Nierlich, et al., eds., Acad. Press, N.Y.,1976); Wu et al., 1978; Khorana, 203 Science 614-25 (1979).

Additionally, DNA synthesis can be achieved through the use of automatedsynthesizers. Techniques of nucleic acid hybridization are disclosed bySambrook et al., 1989, and by Hayrnes et al., in Nucleic AcidHybridization, A Practical Approach (IRL Press, D.C. 1985).Hybridization wash conditions can include wash solution of0.2.times.SSC/0.1% SDS and incubation with rotation for 10 minutes atroom temperature, (low stringency wash), wash solution of prewarmed (42°C.) 0.2×SSC/0.1% SDS and incubation with rotation for fifteen minutes at42° C. (medium stringency wash) and wash solution of prewarmed (68° C.)0.1.times.SSC/0.1% SDS and incubation with rotation for fifteen minutesat 68° C. (high stringency wash). See Ausubel et al., Antibodies: aLaboratory Manual, (Harlow & Lane eds., Cold Spring Harbor Lab., 1988).Techniques such as, or similar to, those described above havesuccessfully enabled the cloning of genes for human aldehydedehydrogenases (Hsu et al., 82 Proc. Natl. Acad. Sci. USA 3771-75(1985)), fibronectin (Suzuki et al., 4 Bur. Mol. Biol. Organ. J. 2519-24(1985)), the human estrogen receptor gene (Walter et al., 82 Proc. Nad.Acad. Sci. USA 7889-93 (1985)), tissue-type plasminogen activator(Pennica et al., 301 Nature 214-21 (1983)) and human term placentalalkaline phosphatase complementary DNA (Keun et al., 82 Proc. Natl. AcadSci. USA 8715-19 (1985)).

It is also intended that the antibody coding regions for use in thepresent invention could also be provided by altering existing antibodygenes using standard molecular biological techniques that result invariants (agonists) of the antibodies and peptides described herein.Such variants include, but are not limited to deletions, additions andsubstitutions in the amino acid sequence of the anti-CPAA antibodies orpeptides.

For example, one class of substitutions is conserved amino acidsubstitutions. Such substitutions are those that substitute a givenamino acid in a anti-CPAA antibody peptide by another amino acid of likecharacteristics. Typically seen as conservative substitutions are thereplacements, one for another, among the aliphatic amino acids Ala, Val,Leu, and Ile; interchange of the hydroxyl residues Ser and Thr, exchangeof the acidic residues Asp and Glu, substitution between the amideresidues Asn and Gln, exchange of the basic residues Lys and Arg,replacements among the aromatic residues Phe, Tyr, and the like.Guidance concerning which amino acid changes are likely to bephenotypically silent is found in Bowie et al., 247 Science 1306-10(1990).

Variant or agonist anti-CPAA antibodies or peptides may be fullyfunctional or may lack function in one or more activities. Fullyfunctional variants typically contain only conservative variations orvariations in non-critical residues or in non-critical regions.Functional variants can also contain substitution of similar amino acidsthat result in no change or an insignificant change in function.Alternatively, such substitutions may positively or negatively affectfunction to some degree.

Non-functional variants typically contain one or more non-conservativeamino acid substitutions, deletions, insertions, inversions, ortruncation or a substitution, insertion, inversion, or deletion in acritical residue or critical region.

Amino acids that are essential for function can be identified by methodsknown in the art, such as site-directed mutagenesis or alanine-scanningmutagenesis. Cunningham et al., 244 Science 1081-85 (1989). The latterprocedure introduces single alanine mutations at every residue in themolecule. The resulting mutant molecules are then tested for biologicalactivity such as epitope binding or in vitro ADCC activity. Sites thatare critical for ligand-receptor binding can also be determined bystructural analysis such as crystallography, nuclear magnetic resonance,or photoaffinity labeling. Smith et al., 224 J. Mol. Biol. 899-904(1992); de Vos et al., 255 Science 306-12 (1992).

Moreover, polypeptides often contain amino acids other than the twenty“naturally occurring” amino acids. Further, many amino acids, includingthe terminal amino acids, may be modified by natural processes, such asprocessing and other post-translational modifications, or by chemicalmodification techniques well known in the art. Known modificationsinclude, but are not limited to, acetylation, acylation,ADP-ribosylation, amidation, covalent attachment of flavin, covalentattachment of a heme moiety, covalent attachment of a nucleotide ornucleotide derivative, covalent attachment of a lipid or lipidderivative, covalent attachment of phosphotidylinositol, cross-linking,cyclization, disulfide bond formation, demethylation, formation ofcovalent crosslinks, formation of cystine, formation of pyroglutamate,formylation, gamma carboxylation, glycosylation, GPI anchor formation,hydroxylation, iodination, methylation, myristoylation, oxidation,proteolytic processing, phosphorylation, prenylation, racemization,selenoylation, sulfation, transfer-RNA mediated addition of amino acidsto proteins such as arginylation, and ubiquitination.

Such modifications are well known to those of skill in the art and havebeen described in great detail in the scientific literature. Severalparticularly common modifications, glycosylation, lipid attachment,sulfation, gamma-carboxylation of glutamic acid residues, hydroxylationand ADP-ribosylation, for instance, are described in most basic texts,such as Proteins—Structure and Molecular Properties (2nd ed., T. E.Creighton, W. H. Freeman and Company, New York 1993). Many detailedreviews are available on this subject, such as by Wold,Posttranslational Covalent Modification of proteins, 1-12 (Johnson, ed.,Academic Press, New York 1983); Seifter et al. 182 Meth. Enzymol. 626-46(1990); and Rattan et al. 663 Ann. N.Y. Acad. Sci. 48-62 (1992).

Accordingly, the antibodies and peptides of the present invention alsoencompass derivatives or analogs in which a substituted amino acidresidue is not one encoded by the genetic code, in which a substituentgroup is included pegylation as mentioned previously.

Similarly, the additions and substitutions in the amino acid sequence aswell as variations, and modifications just described may be equallyapplicable to the amino acid sequence of the CPAA antigen and/or epitopeor peptides thereof, and are thus encompassed by the present invention.As mentioned above, the genes encoding the monoclonal antibody accordingto the present invention is specifically effective in the recognition ofCPAA.

Recombinant Expression of Antibodies

Traditionally, monoclonal antibodies have been produced as nativemolecules in murine hybridoma lines. In addition to that technology,reviewed below, the present invention provides for recombinant DNAexpression of monoclonal antibodies. This allows the production ofhumanized antibodies as well as spectrum of antibody derivatives andfusion proteins in a host species of choice. More recently, theproduction of antibodies in bacteria, yeast, transgenic animals andchicken eggs have emerged as promising alternatives for hybridoma-basedproduction systems. The main advantages of transgenic animals arepotential high yields from renewable sources.

A nucleic acid sequence encoding at least one anti-CPAA antibody,portion or polypeptide of the present invention may be recombined withvector DNA in accordance with conventional techniques, includingblunt-ended or staggered-ended termini for ligation, restriction enzymedigestion to provide appropriate termini, filling in of cohesive ends asappropriate, alkaline phosphatase treatment to avoid undesirablejoining, and ligation with appropriate ligases. Techniques for suchmanipulations are disclosed, e.g., by Maniatis et al., MolecularCloning, A Laboratory Manual, Cold Spring Harbor Lab., Cold SpringHarbor, N.Y. (1982); Sambrook et al. Molecular Cloning: A LaboratoryManual (Cold Spring Harbor Lab. Press 1989), and Ausubel, 1987, 1993,may be used to construct nucleic acid sequences which encode amonoclonal antibody molecule or antigen binding region thereof.

A nucleic acid molecule, such as DNA, is said to be “capable ofexpressing” a polypeptide if it contains nucleotide sequences whichcontain transcriptional and translational regulatory information andsuch sequences are “operably linked” to nucleotide sequences whichencode the polypeptide. An operable linkage is a linkage in which theregulatory DNA sequences and the DNA sequence sought to be expressed areconnected in such a way as to permit gene expression as anti-CPAApeptides or antibody portions in recoverable amounts. The precise natureof the regulatory regions needed for gene expression may vary fromorganism to organism, as is well known in the analogous art. See, e.g.,Sambrook et al., 1989; Ausubel et al., 1987-1993.

The present invention accordingly encompasses the expression of ananti-CPAA antibody or peptide, in either prokaryotic or eukaryoticcells. Suitable hosts include bacterial or eukaryotic hosts includingbacteria, yeast, insects, fungi, bird and mammalian cells either invivo, or in situ, or host cells of mammalian, insect, bird or yeastorigin. The mammalian cell or tissue may be of human, primate, hamster,rabbit, rodent, cow, pig, sheep, horse, goat, dog or cat origin, but anyother mammalian cell may be used.

Further, by use of, for example, the yeast ubiquitin hydrolase system,in vivo synthesis of ubiquitin-transmembrane polypeptide fusion proteinsmay be accomplished. The fusion proteins so produced may be processed invivo or purified and processed in vitro, allowing synthesis of ananti-CPAA antibody or polypeptide of the present invention with aspecified amino terminus sequence. Moreover, problems associated withretention of initiation codon-derived methionine residues in directyeast (or bacterial) expression maybe avoided. Sabin et al., 7 (7)Bio/Technol. 705-09 (1989); Miller et al., 7 (7) Bio/Technol. 698-704(1989).

Any of a series of yeast gene expression systems incorporating promoterand termination elements from the actively expressed genes coding forglycolytic enzymes produced in large quantities when yeast are grown inmediums rich in glucose can be utilized to obtain anti-CPAA antibodiesor peptides of the present invention. Known glycolytic genes can alsoprovide very efficient transcriptional control signals. For example, thepromoter and terminator signals of the phosphoglycerate kinase gene canbe utilized.

Production of anti-CPAA antibodies or peptides or functional derivativesthereof in insects can be achieved, for example, by infecting the insecthost with a baculovirus engineered to express a transmembranepolypeptide by methods known to those of skill. See Ausubel et al.,1987, 1993.

In one embodiment, the introduced nucleotide sequence will beincorporated into a plasmid or viral vector capable of autonomousreplication in the recipient host. Any of a wide variety of vectors maybe employed for this purpose. See, e.g., Ausubel et al., 1987, 1993.Factors of importance in selecting a particular plasmid or viral vectorinclude: the ease with which recipient cells that contain the vector maybe recognized and selected from those recipient cells which do notcontain the vector; the number of copies of the vector which are desiredin a particular host; and whether it is desirable to be able to“shuttle” the vector between host cells of different species.

Example prokaryotic vectors known in the art include plasmids such asthose capable of replication in E. coli (such as, for example, pBR322,ColE1, pSC101, pACYC 184, πVX). Such plasmids are, for example,disclosed by Maniatis et al., 1989; Ausubel et al, 1987, 1993. Bacillusplasmids include pC194, pC221, pT127, etc. Such plasmids are disclosedby Gryczan, in The Molecular Biology of the Bacilli 307-329 (AcademicPress, NY 1982). Suitable Streptomyces plasmids include pIJ101 (Kendallet al., 169 J. Bacteriol. 4177-83 (1987)), and streptomycesbacteriophages such as φC31 (Chater et al., in Sixth Int'l Symposium onActinomycetales Biology 45-54 (Akademiai Kaido, Budapest, Hungary 1986).Pseudomonas plasmids are reviewed by John et al., 8 Rev. Infect. Dis.693-704 (1986); Izaki, 33 Jpn. J. Bacteriol. 729-42 (1978); and Ausubelet al., 1987, 1993.

Alternatively, gene expression elements useful for the expression ofcDNA encoding anti-CPAA antibodies or peptides include, but are notlimited to (a) viral transcription promoters and their enhancerelements, such as the SV40 early promoter (Okayama et al., 3 Mol. Cell.Biol. 280 (1983)), Rous sarcoma virus LTR (Gorman et al., 79 Proc. Natl.Acad. Sci., USA 6777 (1982)), and Moloney murine leukemia virus LTR(Grosschedl et al., 41 Cell 885 (1985)); (b) splice regions andpolyadenylation sites such as those derived from the SV40 late region(Okayarea et al., 1983), and (c) polyadenylation sites such as in SV40(Okayama et al., 1983).

Immunoglobulin cDNA genes can be expressed as described by Liu et al.,infra, and Weidle et al., 51 Gene 21 (1987), using as expressionelements the SV40 early promoter and its enhancer, the mouseimmunoglobulin H chain promoter enhancers, SV40 late region mRNAsplicing, rabbit S-globin intervening sequence, immunoglobulin andrabbit S-globin polyadenylation sites, and SV40 polyadenylationelements.

For immunoglobulin genes comprised of part cDNA, part genomic DNA(Whittle et al., 1 Protein Engineering 499 (1987)), the transcriptionalpromoter can be human cytomegalovirus, the promoter enhancers can becytomegalovirus and mouse/human immunoglobulin, and mRNA splicing andpolyadenylation regions can be the native chromosomal immunoglobulinsequences.

In one embodiment, for expression of cDNA genes in rodent cells, thetranscriptional promoter is a viral LTR sequence, the transcriptionalpromoter enhancers are either or both the mouse immunoglobulin heavychain enhancer and the viral LTR enhancer, the splice region contains anintron of greater than 31 bp, and the polyadenylation and transcriptiontermination regions are derived from the native chromosomal sequencecorresponding to the immunoglobulin chain being synthesized. In otherembodiments, cDNA sequences encoding other proteins are combined withthe above-recited expression elements to achieve expression of theproteins in mammalian cells.

Each fused gene is assembled in, or inserted into, an expression vector.Recipient cells capable of expressing the chimeric immunoglobulin chaingene product are then transfected singly with an anti-CPAA peptide orchimeric H or chimeric L chain-encoding gene, or are co-transfected witha chimeric H and a chimeric L chain gene. The transfected recipientcells are cultured under conditions that permit expression of theincorporated genes and the expressed immunoglobulin chains or intactantibodies or fragments are recovered from the culture.

In one embodiment, the fused genes encoding the anti-CPAA peptide orchimeric H and L chains, or portions thereof, are assembled in separateexpression vectors that are then used to co-transfect a recipient cell.

Each vector can contain two selectable genes, a first selectable genedesigned for selection in a bacterial system and a second selectablegene designed for selection in a eukaryotic system, wherein each vectorhas a different pair of genes. This strategy results in vectors whichfirst direct the production, and permit amplification, of the fusedgenes in a bacterial system. The genes so produced and amplified in abacterial host are subsequently used to co-transfect a eukaryotic cell,and allow selection of a co-transfected cell carrying the desiredtransfected genes.

Examples of selectable genes for use in a bacterial system are the genethat confers resistance to ampicillin and the gene that confersresistance to chloramphenicol. Selectable genes for use in eukaryotictransfectants include the xanthine guanine phosphoribosyl transferasegene (designated gpt) and the phosphotransferase gene from Tn5(designated neo).

Selection of cells expressing gpt is based on the fact that the enzymeencoded by this gene utilizes xanthine as a substrate for purinenucleotide synthesis, whereas the analogous endogenous enzyme cannot. Ina medium containing (1) mycophenolic acid, which blocks the conversionof inosine monophosphate to xanthine monophosphate, and (2) xanthine,only cells expressing the gpt gene can survive. The product of the neoblocks the inhibition of protein synthesis by the antibiotic G418 andother antibiotics of the neomycin class.

The two selection procedures can be used simultaneously or sequentiallyto select for the expression of immunoglobulin chain genes introduced ontwo different DNA vectors into a eukaryotic cell. It is not necessary toinclude different selectable markers for eukaryotic cells; an H and an Lchain vector, each containing the same selectable marker can beco-transfected. After selection of the appropriately resistant cells,the majority of the clones will contain integrated copies of both H andL chain vectors and/or anti-CPAA peptides.

Alternatively, the fused genes encoding the chimeric H and L chains canbe assembled on the same expression vector.

For transfection of the expression vectors and production of thechimeric antibody, the recipient cell line may be a myeloma cell.Myeloma cells can synthesize, assemble and secrete immunoglobulinsencoded by transfected immunoglobulin genes and possess the mechanismfor glycosylation of the immunoglobulin. For example the recipient cellis the recombinant Ig-producing myeloma cell SP2/0 (ATCC #CRL 8287).SP2/0 cells produce only immunoglobulin encoded by the transfectedgenes. Myeloma cells can be grown in culture or in the peritoneal cavityof a mouse, where secreted immunoglobulin can be obtained from ascitesfluid. Other suitable recipient cells include lymphoid cells such as Blymphocytes of human or non-human origin, hybridoma cells of human ornon-human origin, or interspecies heterohybridoma cells.

The expression vector carrying a chimeric antibody construct oranti-CPAA polypeptide of the present invention can be introduced into anappropriate host cell by any of a variety of suitable means, includingsuch biochemical means as transformation, transfection, conjugation,protoplast fusion, calcium phosphate-precipitation, and application withpolycations such as diethylaminoethyl (DEAE) dextran, and suchmechanical means as electroporation, direct microinjection, andmicroprojectile bombardment. Johnston et al., 240 Science 1538 (1988).

Another way of introducing DNA into lymphoid cells is byelectroporation. Potter et al., 81 Proc. Natl. Acad. Sci. USA 7161(1984); Yoshikawa et al., 77 Jpn. J. Cancer Res. 1122-33 (1986). In thisprocedure, recipient cells are subjected to an electric pulse in thepresence of the DNA to be incorporated. Typically, after transfection,cells are allowed to recover in complete medium for about 24 hours, andare then seeded in 96-well culture plates in the presence of theselective medium. G418 selection is performed using about 0.4 to 0.8mg/ml G418. Mycophenolic acid selection utilizes about 6 μg/ml plusabout 0.25 mg/ml xanthine. The electroporation technique is expected toyield transfection frequencies of about 10⁻⁵ to about 10⁻⁴ for Sp^(2/0)cells. In the protoplast fusion method, lysozyme is used to strip cellwalls from catarrhal harboring the recombinant plasmid containing thechimeric antibody gene. The resulting spheroplasts are fused withmyeloma cells with polyethylene glycol.

The immunoglobulin genes of the present invention can also be expressedin nonlymphoid mammalian cells or in other eukaryotic cells, such asyeast, or in prokaryotic cells, in particular bacteria.

Yeast provides substantial advantages over bacteria for the productionof immunoglobulin H and L chains. Yeasts carry out post-translationalpeptide modifications including glycosylation. A number of recombinantDNA strategies now exist which utilize strong promoter sequences andhigh copy number plasmids which can be used for production of thedesired proteins in yeast. Yeast recognizes leader sequences of clonedmammalian gene products and secretes peptides bearing leader sequences(i.e., pre-peptides). Hitzman et al., 11th Int'l Conference on Yeast,Genetics & Molecular Biol. (Montpelier, France, 1982).

Yeast gene expression systems can be routinely evaluated for the levelsof production, secretion and the stability of anti-CPAA peptides,antibody and assembled murine and chimeric antibodies, fragments andregions thereof. Any of a series of yeast gene expression systemsincorporating promoter and termination elements from the activelyexpressed genes coding for glycolytic enzymes produced in largequantities when yeasts are grown in media rich in glucose can beutilized. Known glycolytic genes can also provide very efficienttranscription control signals. For example, the promoter and terminatorsignals of the phosphoglycerate kinase (PGK) gene can be utilized. Anumber of approaches can be taken for evaluating optimal expressionplasmids for the expression of cloned immunoglobulin cDNAs in yeast. SeeII DNA Cloning, 45-66, (Glover, ed., IRL Press, 1985).

Bacterial strains can also be utilized as hosts for the production ofantibody molecules or peptides described by this invention, E. coli K12strains such as E. coli W3110 (ATCC 27325), and other enterobacteriasuch as Salmonella typhimurium or Serratia marcescens, and variousPseudomonas species can be used.

Plasmid vectors containing replicon and control sequences which arederived from species compatible with a host cell are used in connectionwith these bacterial hosts. The vector carries a replication site, aswell as specific genes which are capable of providing phenotypicselection in transformed cells. A number of approaches can be taken forevaluating the expression plasmids for the production of murine andchimeric antibodies, fragments and regions or antibody chains encoded bythe cloned immunoglobulin cDNAs in bacteria (see Glover, 1985; Ausubel,1987, 1993; Sambrook, 1989; Colligan, 1992-1996).

Host mammalian cells may be grown in vitro or in vivo. Mammalian cellsprovide post-translational modifications to immunoglobulin proteinmolecules including leader peptide removal, folding and assembly of Hand L chains, glycosylation of the antibody molecules, and secretion offunctional antibody protein.

Mammalian cells which can be useful as hosts for the production ofantibody proteins, in addition to the cells of lymphoid origin describedabove, include cells of fibroblast origin, such as Vero (ATCC CRL 81) orCHO-K1 (ATCC CRL 61).

Many vector systems are available for the expression of cloned anti-CPAApeptides H and L chain genes in mammalian cells (see Glover, 1985).Different approaches can be followed to obtain complete H₂ L₂antibodies. As discussed above, it is possible to co-express H and Lchains in the same cells to achieve intracellular association andlinkage of H and L chains into complete tetrameric H₂ L₂ antibodiesand/or anti-CPAA peptides. The co-expression can occur by using eitherthe same or different plasmids in the same host. Genes for both H and Lchains and/or anti-CPAA peptides can be placed into the same plasmid,which is then transfected into cells, thereby selecting directly forcells that express both chains. Alternatively, cells can be transfectedfirst with a plasmid encoding one chain, for example the L chain,followed by transfection of the resulting cell line with an H chainplasmid containing a second selectable marker. Cell lines producinganti-CPAA peptides and/or H₂ L₂ molecules via either route could betransfected with plasmids encoding additional copies of peptides, H, L,or H plus L chains in conjunction with additional selectable markers togenerate cell lines with enhanced properties, such as higher productionof assembled H₂ L₂ antibody molecules or enhanced stability of thetransfected cell lines.

Additionally, plants have emerged recently as a convenient, safe andeconomical alternative main-stream expression systems for recombinantantibody production, which are based on large scale culture of microbesor animal cells. Antibodies may be expressed in plant cell culture, orplants grown conventionally. The expression in plants may be systemic,limited to susb-cellular plastids, or limited to seeds (endosperms).See, e.g., U.S. Patent Appl. Pub. No. 20030167531; U.S. Pat. No.6,080,560 and No. 6,512,162; and WO 0129242. Several plant-derivedantibodies have reached advanced stages of development, includingclinical trials (see, e.g., Biolex, NC).

Hybridoma Technology

The present invention provides for a hybridoma cell line that produces amonoclonal antibody that has a high degree of specificity and affinitytowards CPAA. The present invention relates also to variants and mutantsof the hybridoma cell lines characterised in detail above that occurspontaneously or that can be produced artificially using known methodsand that still have the characteristic properties of the startingmaterial, that is to say are still capable of producing the antibodiesaccording to the invention or derivatives thereof and secreting theminto the surrounding medium.

The present invention also includes methods for the production of saidhybridoma cell lines and to methods for the production of saidmonoclonal antibodies. Clones and sub-clones of hybridoma cell lines areto be understood as being hybridomas that are produced from the startingclone by repeated cloning and that still have the features of thestarting clone that are essential to the invention.

More specifically, nucleic acid, protein or peptide molecules of theinvention may be utilized to develop monoclonal or polyclonal antibodiesthat bind CPAA. For preparation of the CPAA-binding antibodies of thepresent invention, any technique which provides for the production ofantibody molecules by continuous cell lines in culture may be used. Forexample, the hybridoma technique originally developed by Kohler andMilstein (256 Nature 495-497 (1975)) may be used. See also U.S. Pat. No.4,376,110; Ausubel et al., Antibodies: a Laboratory Manual, (Harlow &Lane eds., Cold Spring Harbor Lab. 1988); Current Protocols inImmunology, (Colligan et al., eds., Greene Pub. Assoc. & WileyInterscience N.Y., 1992-1996).

Another advantageous route for creating high affinity and/or highavidity human antibodies involves antigen priming of native humansplenocytes in vitro, transferral of the resultant in vitro antigenprimed splenocyte cells to an immunocompromised donor, e.g., a SCIDmouse, boosting the immunocompromised donor with antigen, isolatinghuman antibody secreting B-cells (IgG secreting) from the donor, andEBV-transforming the isolated human antibody secreting cells, asdescribed in U.S. Pat. No. 6,537,809.

Chimeric Humanized and Fully Humanized Antibodies

The antibodies of the present invention include chimeric antibodiescomprising part human and part mouse antibodies, in which the constantregion from human antibodies are cloned to a variable regions of lightand heavy chains from mouse. In some instances, 70% of the humansequences are retained. Humanized antibodies are chimeric antibodies inwhich perhaps 90% of the human antibody framework is retained, andcombined only with the murine the complementary determining regions.Fully humanized antibodies are also contemplated in the presentinvention.

Recombinant murine or chimeric murine-human or human-human antibodiesthat bind an epitope included in the amino acid sequences of CPAA can beprovided according to the present invention using known techniques basedon the teaching provided herein. See, e.g., Current Protocols inMolecular Biology (Ausubel et al., eds. Wiley Interscience, N.Y., 1987,1992, 1993); Sambrook et al. Molecular Cloning: A Laboratory Manual(Cold Spring Harbor Lab. Press 1989). For example, an antibody may behumanized by grafting the desired CDRs onto a human framework accordingto EP0239400.

The DNA encoding an anti-CPAA antibody of the present invention can begenomic DNA or cDNA which encodes at least one of the heavy chainconstant region (H_(c)), the heavy chain variable region (H_(v)), thelight chain variable region (L_(v)) and the light chain constant regions(L_(c)). A convenient alternative to the use of chromosomal genefragments as the source of DNA encoding the murine V regionantigen-binding segment is the use of cDNA for the construction ofchimeric immunoglobulin genes. See e.g., Liu et al. 84 Proc. Natl. Acad.Sci., USA 3439 (1987); 139 J. Immunology 3521 (1987). The use of cDNArequires that gene expression elements appropriate for the host cell becombined with the gene in order to achieve synthesis of the desiredprotein. The use of cDNA sequences is advantageous over genomicsequences (which contain introns), in that cDNA sequences can beexpressed in bacteria or other hosts which lack appropriate RNA splicingsystems.

For example, a cDNA encoding murine V and C region antigen-bindingsegments having anti-CPAA activity can be provided using known methodsbased on the use of the DNA sequences presented in FIG. 2-FIG. 5 (SEQ IDNOS:1-2, 4-5). Probes that bind a portion of the DNA sequences presentedin FIG. 2 (SEQ ID NO:1) or FIG. 4 (SEQ ID NO:4) can be used to isolateDNA from hybridomas expressing anti-CPAA antibodies, fragments orregions, as presented herein, according to the present invention, byknown methods.

Oligonucleotides representing the CPAA-binging antibodies light andheavy chains, presented in FIG. 2-FIG. 5 (SEQ ID NOS:1-2, 4-5) usefulfor screening for the presence of homologous genes and for the cloningof such genes encoding variable or constant regions of an anti-CPAAantibody. Such probes usually bind to DNA sequences (cDNA, genomic DNA,or any other DNA) that encode the amino acid sequences depicted in FIG.6 (SEQ ID NO:3) and FIG. 7 (SEQ ID NO:6) to the light chain or heavychain CDR regions which bind an epitope of CPAA. Such techniques forsynthesizing such oligonucleotides are well known. See e.g., Wu et al.,21 Prog. Nucl. Acid. Res. Molec. Biol. 101-41 (1978); Ausubel et al.,1987, 1993.

In an alternative way of cloning a polynucleotide encoding an anti-CPAAvariable or constant region, a library of expression vectors is preparedby cloning DNA or cDNA (from a cell capable of expressing an anti-CPAAantibody or variable or constant region) into an expression vector. Thelibrary is then screened for members capable of expressing a proteinwhich competitively inhibits the binding of an anti-CPAA antibody, suchas A2 or cA2, and which has a nucleotide sequence that is capable ofencoding peptides that have the same amino acid sequence as anti-CPAAantibodies or fragments thereof. In this embodiment, DNA, such as cDNA,is extracted and purified from a cell which is capable of expressing ananti-CPAA antibody or fragment. The purified cDNA is fragmentized (byshearing, endonuclease digestion, etc.) to produce a pool of DNA or cDNAfragments. DNA or cDNA fragments from this pool are then cloned into anexpression vector in order to produce a genomic library of expressionvectors whose members each contain a unique cloned DNA or cDNA fragmentsuch as in a lambda phage library, expression in prokaryotic cell (e.g.,bacteria) or eukaryotic cells, (e.g., mammalian, yeast, insect or,fungus). See, e.g., Ausubel, 1987, 1993; Harlow, 1988; Colligan,1992-1996; Nyyssonen et al. 11 Bio/Technology 591-95 (1993); Marks etal., 11 Bio/Technology 1145-49 (1993).

Once nucleic acid encoding such variable or constant anti-CPAA regionsis isolated, the nucleic acid can be appropriately expressed in a hostcell, along with other constant or variable heavy or light chainencoding nucleic acid, in order to provide recombinant monoclonalantibodies that bind CPAA with inhibitory activity. Such antibodies mayinclude a murine or human anti-CPAA variable region which contains aframework residue having complementarity determining residues which areresponsible for antigen binding. In one embodiment, an anti-CPAAvariable light or heavy chain encoded by a nucleic acid as describedabove binds an epitope of at least five amino acids. The amino acidsequences of such anti-CPAA variable light or heavy chains are depictedin FIG. 6 (SEQ ID NO:3) and FIG. 7 (SEQ ID NO:6).

Human genes which encode the constant (C) regions of the murine andchimeric antibodies, fragments and regions of the present invention canbe derived from a human fetal liver library, by known methods. Human Cregions genes can be derived from any human cell including those whichexpress and produce human immunoglobulins. The human C_(H) region can bederived from any of the known classes or isotypes of human H chains,including γ, μ, α, δ or ε, and subtypes thereof, such as G1, G2, G3 andG4. Since the H chain isotype is responsible for the various effectorfunctions of an antibody, the choice of C_(H) region will be guided bythe desired effector functions, such as complement fixation, or activityin antibody-dependent cellular cytotoxicity (ADCC). For example, theC_(H) region is derived from gamma 1 (IgG1), gamma 3 (IgG3), gamma 4(IgG4), or μ (IgM). The human C_(L) region can be derived from eitherhuman L chain isotype, kappa or lambda.

Genes encoding human immunoglobulin C regions are obtained from humancells by standard cloning techniques (Sambrook et al., 1989; Ausubel etal., 1987, 1993). Human C region genes are readily available from knownclones containing genes representing the two classes of L chains, thefive classes of H chains and subclasses thereof. Chimeric antibodyfragments, such as F(ab′)₂ and Fab, can be prepared by designing achimeric H chain gene which is appropriately truncated. For example, achimeric gene encoding an H chain portion of an F(ab′)₂ fragment wouldinclude DNA sequences encoding the CH₁ domain and hinge region of the Hchain, followed by a translational stop codon to yield the truncatedmolecule.

Generally, the murine, human or murine and chimeric antibodies,fragments and regions of the present invention are produced by cloningDNA segments encoding the H and L chain antigen-binding regions of aCPAA-specific antibody, and joining these DNA segments to DNA segmentsencoding C_(H) and C_(L) regions, respectively, to produce murine, humanor chimeric immunoglobulin-encoding genes.

Thus, in one embodiment, a fused chimeric gene is created whichcomprises a first DNA segment that encodes at least the antigen-bindingregion of non-human origin, such as a functionally rearranged V regionwith joining (J) segment, linked to a second DNA segment encoding atleast a part of a human C region.

Therefore, cDNA encoding the antibody V and C regions, the method ofproducing the chimeric antibody according to the present inventioninvolves several steps, outlined below:

1. isolation of messenger RNA (mRNA) from the cell line producing ananti-CPAA antibody and from optional additional antibodies supplyingheavy and light constant regions; cloning and cDNA production therefrom;

2. preparation of a full length cDNA library from purified mRNA fromwhich the appropriate V and/or C region gene segments of the L and Hchain genes can be: (i) identified with appropriate probes, (ii)sequenced, and (iii) made compatible with a C or V gene segment fromanother antibody for a chimeric antibody;

3. Construction of complete H or L chain coding sequences by linkage ofthe cloned specific V region gene segments to cloned C region gene, asdescribed above;

4. Expression and production of L and H chains in selected hosts,including prokaryotic and eukaryotic cells to provide murine-murine,human-murine, human-human or human murine antibodies.

One common feature of all immunoglobulin H and L chain genes and theirencoded mRNAs is the J region. H and L chain J regions have differentsequences, but a high degree of sequence homology exists (greater than80%) among each group, especially near the C region. This homology isexploited in this method and consensus sequences of H and L chain Jregions can be used to design oligonucleotides for use as primers forintroducing useful restriction sites into the J region for subsequentlinkage of V region segments to human C region segments.

C region cDNA vectors prepared from human cells can be modified bysite-directed mutagenesis to place a restriction site at the analogousposition in the human sequence. For example, one can clone the completehuman kappa chain C (C_(k)) region and the complete human gamma-1 Cregion (C_(γ-1)). In this case, the alternative method based upongenomic C region clones as the source for C region vectors would notallow these genes to be expressed in bacterial systems where enzymesneeded to remove intervening sequences are absent. Cloned V regionsegments are excised and ligated to L or H chain C region vectors.Alternatively, the human C_(γ-1) region can be modified by introducing atermination codon thereby generating a gene sequence which encodes the Hchain portion of a Fab molecule. The coding sequences with linked V andC regions are then transferred into appropriate expression vehicles forexpression in appropriate hosts, prokaryotic or eukaryotic.

Two coding DNA sequences are said to be “operably linked” if the linkageresults in a continuously translatable sequence without alteration orinterruption of the triplet reading frame. A DNA coding sequence isoperably linked to a gene expression element if the linkage results inthe proper function of that gene expression element to result inexpression of the coding sequence.

Expression vehicles include plasmids or other vectors. Among these arevehicles carrying a functionally complete human C_(H) or C_(L) chainsequence having appropriate restriction sites engineered so that anyV_(H) or V_(L) chain sequence with appropriate cohesive ends can beeasily inserted therein. Human C_(H) or C_(L) chain sequence-containingvehicles thus serve as intermediates for the expression of any desiredcomplete H or L chain in any appropriate host.

A chimeric antibody, such as a mouse-human or human-human, willtypically be synthesized from genes driven by the chromosomal genepromoters native to the mouse H and L chain V regions used in theconstructs; splicing usually occurs between the splice donor site in themouse J region and the splice acceptor site preceding the human C regionand also at the splice regions that occur within the human C region;polyadenylation and transcription termination occur at nativechromosomal sites downstream of the human coding regions. See U.S. Pat.No. 6,835,823.

“Fully humanized antibodies” against CPAA are also contemplated in thepresent invention. Fully humanized antibodies are molecules containingboth the variable and constant region of the human immunoglobulin. Fullyhumanized antibodies can be potentially used for therapeutic use, whererepeated treatments are required for chronic and relapsing diseases suchas autoimmune diseases. One method for the preparation of fully humanantibodies consist of “humanization” of the mouse humoral immune system,i.e. production of mouse strains able to produce human Ig (Xenomice), bythe introduction of human immunoglobulin (Ig) loci into mice in whichthe endogenous Ig genes have been inactivated. The Ig loci areexceedingly complex in terms of both their physical structure and thegene rearrangement and expression processes required to ultimatelyproduce a broad immune response. Antibody diversity is primarilygenerated by combinatorial rearrangement between different V, D, and Jgenes present in the Ig loci. These loci also contain the interspersedregulatory elements, which control antibody expression, allelicexclusion, class switching and affinity maturation. Introduction ofunrearranged human Ig transgenes into mice has demonstrated that themouse recombination machinery is compatible with human genes.Furthermore, hybridomas secreting antigen specific hu-mAbs of variousisotypes can be obtained by Xenomice immunization with antigen. Fullyhumanized antibodies and methods for their production are known in theart. See, e.g., U.S. Pat. No. 6,835,823.

An aspect of the present invention provides for the production of ahumanized antibody, which is prepared according to the invention by aprocess which comprises maintaining a host transformed with a firstexpression vector which encodes the light chain of the humanizedantibody and with a second expression vector which encodes the heavychain of the humanized antibody under such conditions that each chain isexpressed and isolating the humanized antibody formed by assembly of thethus-expressed chains. The first and second expression vectors may bethe same vector. The invention further provides: a DNA sequence encodingthe light chain or the heavy chain of the humanized antibody; anexpression vector which incorporates a said DNA sequence; and a hosttransformed with a said expression vector.

Generating a humanized antibody from the sequences provided herein canbe practiced by those of ordinary skill in the art without undueexperimentation. There are four general steps to humanize a monoclonalantibody, see, e.g., U.S. Pat. No. 5,585,089; No. 6,835,823; and No.6,824,989. These are: (1) determining the nucleotide and predicted aminoacid sequence of the starting antibody light and heavy variable domains;(2) designing the humanized antibody, i.e., deciding which antibodyframework region to use during the humanizing process; (3) the actualhumanizing methodologies/techniques; and (4) the transfection andexpression of the humanized antibody.

Regarding the nucleotide and predicted amino acid sequences, there aretwo general methods for cloning a given antibody's heavy and light chainvariable domain cDNAs: (a) via a conventional cDNA library, or (b) viathe polymerase chain reaction (PCR). Both of these methods are widelyknown, see, e.g., U.S. Patent Appl. Pub. No. 2003/0166871. Given thenucleotide sequence of the cDNAs, it is a simple matter to translatethis information into the predicted amino acid sequence of the antibodyvariable domains. In the present instance, the nucleotide sequence andpredicted amino acid sequence of the light and heavy chains of the NPC-1antibody are shown in FIG. 2 (SEQ ID NOS:2-3) and FIG. 5 (SEQ IDNOS:5-6), respectively.

Regarding the design of the humanized antibody, there are severalfactors to consider in deciding which human antibody sequence to useduring the humanization. The humanization of light and heavy chains areconsidered independently of one another, but the reasoning is basicallysimilar for each. This selection process is based on the followingrationale: A given antibody's antigen specificity and affinity isprimarily determined by the amino acid sequence of the variable regionCDRs. Variable domain framework residues have little or no directcontribution. The primary function of the framework regions is to holdthe CDRs in their proper spatial orientation to recognize antigen. Thus,the substitution of rodent CDRs such as those presented in FIG. 6 andSEQ ID NOS:7-9 or FIG. 7 and (SEQ ID NOS:10-12), into a human variabledomain framework is most likely to result in retention of their correctspatial orientation if the human variable domain framework is highlyhomologous to the rodent variable domain from which they originated. Ahuman variable domain should be chosen, therefore, that is highlyhomologous to the rodent variable domain(s).

A suitable human antibody variable domain sequence can be selected asfollows:

1. Using a computer program, search all available protein (and DNA)databases for those human antibody variable domain sequences that aremost homologous to the rodent antibody variable domains. The output of asuitable program is a list of sequences most homologous to the rodentantibody, the percent homology to each sequence, and an alignment ofeach sequence to the rodent sequence. This is done independently forboth the heavy and light chain variable domain sequences. The aboveanalyses are more easily accomplished if only human immunoglobulinsequences are included.

2. List the human antibody variable domain sequences and compare forhomology. Primarily, the comparison is performed on length of CDRs,except CDR3 of the heavy chain which is quite variable. Human heavychains and Kappa and Lambda light chains are divided into subgroups;Heavy chain 3 subgroups, Kappa chain 4 subgroups, Lambda chain 6subgroups. The CDR sizes within each subgroup are similar but varybetween subgroups. It is usually possible to match a rodent antibody CDRto one of the human subgroups as a first approximation of homology.Antibodies bearing CDRs of similar length are then compared for aminoacid sequence homology, especially within the CDRs, but also in thesurrounding framework regions. The human variable domain which is mosthomologous is chosen as the framework for humanization.

The actual humanizing methodologies and techniques are also within thegrasp of those of ordinary skill in the art. A DNA sequence encoding thedesired reshaped antibody can therefore be made beginning with the humanDNA whose CDRs it is wished to reshape. The rodent variable domain aminoacid sequence containing the desired CDRs is compared to that of thechosen human antibody variable domain sequence. The residues in thehuman variable domain are marked that need to be changed to thecorresponding residue in the rodent to make the human variable regionincorporate the rodent CDRs. There may also be residues that needsubstituting in, adding to or deleting from the human sequence.

Oligonucleotides are synthesized that can be used to mutagenize thehuman variable domain framework to contain the desired residues. Thoseoligonucleotides can be of any convenient size. One is normally onlylimited in length by the capabilities of the particular synthesizer onehas available. The method of oligonucleotide-directed in vitromutagenesis is well known.

Alternatively, humanization may be achieved using the recombinantpolymerase chain reaction (PCR) methodology of U.S. Pat. No. 5,858,725.Using this methodology, a CDR may be spliced between the frameworkregions of a human antibody. In general, the technique of U.S. Pat. No.5,858,725 can be performed using a template comprising two humanframework regions, AB and CD, and between them, the CDR which is to bereplaced by a donor CDR. Primers A and B are used to amplify theframework region CD. However, the primers B and C each also contain, attheir 5′ ends, an additional sequence corresponding to all or at leastpart of the donor CDR sequence. Primers B and C overlap by a lengthsufficient to permit annealing of their 5′ ends to each other underconditions which allow a PCR to be performed. Thus, the amplifiedregions AB and CD may undergo gene splicing by overlap extension toproduce the humanized product in a single reaction.

Following the mutagenesis reactions to reshape the antibody, themutagenized DNAs can be linked to an appropriate DNA encoding a light orheavy chain constant region, cloned into an expression vector, andtransfected into host cells, such as mammalian cells. These steps can becarried out in routine fashion. A reshaped antibody may therefore beprepared by a process comprising:

(a) preparing a first replicable expression vector including a suitablepromoter operably linked to a DNA sequence which encodes at least avariable domain of an Ig heavy or light chain, the variable domaincomprising framework regions from a human antibody and the CDRs requiredfor the humanized antibody of the invention;

(b) preparing a second replicable expression vector including a suitablepromoter operably linked to a DNA sequence which encodes at least thevariable domain of a complementary Ig light or heavy chain,respectively;

(c) transforming a cell line with the first or both prepared vectors;and

(d) culturing said transformed cell line to produce said alteredantibody.

The DNA sequence in step (a) may encode both the variable domain and/oreach constant domain of the human antibody chain. The humanized antibodycan be prepared using any suitable recombinant expression system. Thecell line that is transformed to produce the altered antibody may be aChinese Hamster Ovary (CHO) cell line or an immortalized mammalian cellline, which is advantageously of lymphoid origin, such as a myeloma,hybridoma, trioma or quadroma cell line. The cell line may also comprisea normal lymphoid cell, such as a B-cell, which has been immortalized bytransformation with a virus, such as the Epstein-Barr virus. Forexample, the immortalized cell line is a myeloma cell line or aderivative thereof.

The CHO cells used for expression of the antibodies according to theinvention may be dihydrofolate reductase (dhfr) deficient and sodependent on thymidine and hypoxanthine for growth. See Urlaub et al.,77 Proc. Natl. Acad. Sci. U.S.A. 4216-20 (1980). The parental dhfr CHOcell line is transfected with the DNA encoding the antibody and dhfrwhich enables selection of CHO cell transfectants of dhfr positivephenotype. Selection is carried out by culturing the colonies on mediadevoid of thymidine and hypoxanthine, the absence of which preventsuntransfected cells from growing and transformed cells from resalvagingthe folate pathway and thus bypassing the selection system. Thesetransfectants usually express low levels of the DNA of interest byvirtue of co-integration of transfected DNA of interest and DNA encodingdhfr. The expression levels of the DNA encoding the antibody may beincreased by amplification using methotrexate (MTX). This drug is adirect inhibitor of the enzyme dhfr and allows isolation of resistantcolonies which amplify their dhfr gene copy number sufficiently tosurvive under these conditions. Since the DNA sequences encoding dhfrand the antibody are closely linked in the original transfectants, thereis usually concomitant amplification, and therefore increased expressionof the desired antibody.

Another expression system for use with CHO or myeloma cells is theglutamine synthetase (GS) amplification system described in U.S. Pat.No. 5,122,464. This system involves the transfection of a cell with DNAencoding the enzyme GS and with DNA encoding the desired antibody. Cellsare then selected which grow in glutamine free medium and can thus beassumed to have integrated the DNA encoding GS. These selected clonesare then subjected to inhibition of the enzyme GS using methioninesulphoximine (Msx). The cells, in order to survive, will amplify the DNAencoding GS with concomitant amplification of the DNA encoding theantibody.

Although the cell line used to produce the humanized antibody may be amammalian cell line, any other suitable cell line, such as a bacterialcell line or a yeast cell line, may alternatively be used. For example,in instances requiring no in vivo post-translational modification (suchas instances where glycosylation is not required), it is envisaged thatE. coli-derived bacterial strains could be used. The antibody obtainedis checked for functionality. If functionality is lost, it is necessaryto return to step (2) and alter the framework of the antibody.

Once expressed, the whole antibodies, their dimers, individual light andheavy chains, or other immunoglobulin forms of the present invention canbe recovered and purified by known techniques, e.g., immunoabsorption orimmunoaffinity chromatography, chromatographic methods such as HPLC(high performance liquid chromatography), ammonium sulfateprecipitation, gel electrophoresis, or any combination of these. Seegenerally, Scopes, PROTEIN PURIFICATION (Springer-Verlag, NY, 1982).Substantially pure immunoglobulins of at least about 90% to 95%homogeneity are advantageous, as are those with 98% to 99% or morehomogeneity, particularly for pharmaceutical uses. Once purified,partially or to homogeneity as desired, a humanized antibody may then beused therapeutically or in developing and performing assay procedures,immunofluorescent stainings, and the like. See generally, Vols. I & IIImmunological Methods, (Lefkovits & Pernis, eds., Academic Press, NY,1979 and 1981).

Phage Libraries and Alternative Recombinant Expression Systems

Along with the above production techniques, in vitro systems such asphage display methods of fully human antibodies and antibody peptides,many of the benefits of human antibodies as both diagnostics andtherapeutics are now being realized.

The recombinant antibody and its sequences of the present inventionallows for the construction of a myriad of derivatives and ligandbinding molecules with anti-PCAA binding activity. For example, the CDRsmay be recombined with an antibody library such as the n-CoDeR humanscFV library to create highly specific and functional antibodyfragments. See Moore, 426 Nature, 725-31 (2003).

A library of fully human antibodies or portions thereof may also becreated following the cloning methods based on site specific cleavage ofsingle-stranded DNAs as described by U.S. Patent Appl. Ser. No.20030232333.

Another ligand binding molecule that may be constructed from the DNAsequence information contained herein, and the associated knowledgegained about the PCAA epitopes provided by the invention herein,involves the construction of ANTICALINS® (lipocalins, muteins).ANTICALINS are derived from lipocalins, a widespread group of small androbust proteins that are usually involved in the physiological transportor storage of chemically sensitive or insoluble compounds. Severalnatural lipocalins occur in human tissues or body liquids. Despite lowmutual sequence homology, the lipocalins share a structurally conservedβ-barrel supporting four loops at one end, which form the entrance to abinding pocket. The loops exhibit large conformational differencesbetween individual lipocalins and give rise to the variety of naturalligand specificities. This protein architecture is reminiscent ofimmunoglobulins, with their hypervariable loops on top of a rigidframework. Unlike antibodies or some antibody fragments, lipocalins arecomposed of a single polypeptide chain with 160 to 180 amino acidresidues, being just marginally bigger than a single immunoglobulindomain. The set of four loops that makes up the binding pocket showsstructural plasticity and tolerates a variety of side chains. Thebinding site can thus be reshaped in order to recognize prescribedtarget molecules of different shape with high affinity and specificity.ANTICALINS® have been engineered that recognize hapten-like compounds,peptides, and protein targets, e.g. extracellular domains of cellsurface receptors. Fusion proteins with enzymes and also bispecificbinding proteins (so-called DUOCALINS®) have also been successfullyprepared. Pre-clinical experiments have been conducted. See, e.g.,Korndörfer et al., 330 J. Mol. Biol. 385-96 (2003).

Another antibody type with application to the invention described hereininclude the camilid immunoglobulins which possess functional heavychains and lack light chains. These antibodies are assembled fromdedicated V and C gamma genes. They have been cloned and adapted usingphage display technology to produce antigen-specific single-domainantibody fragments with intrinsic high stability. U.S. Patent Appl. Pub.No. 2003/0088074.

Another relevant derivative takes advantage of new technology forproviding bacterially produced antibody fragments that can crosslinkantigen and antibody effector molecules (Fc-region molecules), calledPepbodies™. U.S. Patent Appl. Pub. No. 20040101905. Hence, the bindingmolecules comprising the antigen binding site of the anti-PCAA site isgenetically fused to peptides that display one or more of the effectorfunctions associated with the Fc-region, and provides for functions suchas interaction with cell receptors and complement activation.

The new antigen receptor (IgNAR) molecules from sharks may also beconsidered a “derivative” antibody molecule. The NAR is a disulphidebonded dimer of two protein chains, each containing one variable andfive constant domains, and functions as an antibody. Nuttall et al., 270Eur. J. Biochem., 3543-54 (2003). The sequences of the PCAA-bindingantibody of the present invention may be constructed into the NARvariable region to create an in vitro library incorporating syntheticthe CDR regions. This results in a single domain binding reagent.

One of the recent advances in cancer cell biology entails the discoveryof progenitor cell lines that may exhibit cancer-cell markers. Forexample, human pancreatic epithelial progenitor cells have beenidentified and grown in culture. These cells may then be used for thegeneration of antigens useful, inter alia, for the development ofmonoclonal antibodies. U.S. Pat. No. 6,436,704. Thus, the PCAA-bindingantibody may be used to identify progenitor cells. These progenitorcells can be used as an immunogen that is administered to a heterologousrecipient, such as a mouse, for derivation of further lines ofPCAA-binding antibodies.

In conclusion, the oligonucleotide and amino acid sequences providedherein enable a myriad of possible molecules with CPAA-binding activity,and the scope of the present invention is not limited by the methods ofachieving those molecules.

Antibody Derivatives

A “derivative” of an antibody contains additional chemical moieties notnormally a part of the protein. Covalent modifications of the proteinare included within the scope of this invention. Such modifications maybe introduced into the molecule by reacting targeted amino acid residuesof the antibody with an organic derivatizing agent that is capable ofreacting with selected side chains or terminal residues. For example,derivatization with bifunctional agents, well-known in the art, isuseful for cross-linking the antibody or fragment to a water-insolublesupport matrix or to other macromolecular carriers.

Derivatives also include radioactively labelled monoclonal antibodiesthat are labeled, for example, with radioactive iodine (¹²⁵I, ¹³¹I),carbon (¹⁴C), sulfur (³⁵S), tritium (³H) or the like; conjugates ofmonoclonal antibodies with biotin or avidin, with enzymes, such ashorseradish peroxidase, alkaline phosphatase, β-D-galactosidase, glucoseoxidase, glucoamylase, carboxylic acid anhydrase, acetylcholineesterase, lysozyme, malate dehydrogenase or glucose 6-phosphatedehydrogenase; and also conjugates of monoclonal antibodies withbioluminescent agents (such as luciferase), chemiluminescent agents(such as acridine esters) or fluorescent agents (such asphycobiliproteins). An example of a derivative of the antibody of theinvention is an antibody-small molecule drug conjugate, such as anantibody-maytansinoid conjugate, that displays cytotoxic activity. SeeU.S. Patent Appl. Pub. No. 20040039176. Preclinical evaluation has shownthat this conjugate acts as a tumor-activated prodrug that exhibitspotent antitumor activity in xenograft models. Further cytotoxicantibody derivatives are discussed below.

Another derivative bifunctional antibody of the present invention is abispecific antibody, generated by combining parts of two separateantibodies that recognize two different antigenic groups. This may beachieved by crosslinking or recombinant techniques. Additionally,moieties may be added to the antibody or a portion thereof to increasehalf-life in vivo (e.g., by lengthening the time to clearance from theblood stream. Such techniques include, for example, adding PEG moieties(also termed pegilation), and are well-known in the art. See U.S.Patent. Appl. Pub. 20030031671.

Anti-Idiotype Abs

In addition to monoclonal or chimeric anti-CPAA antibodies, the presentinvention is also directed to an anti-idiotypic (anti-Id) antibodyspecific for the anti-CPAA antibody of the invention. An anti-Idantibody is an antibody which recognizes unique determinants generallyassociated with the antigen-binding region of another antibody. Theantibody specific for CPAA is termed the idiotypic or Id antibody. Theanti-Id can be prepared by immunizing an animal of the same species andgenetic type (e.g. mouse strain) as the source of the Id antibody withthe Id antibody or the antigen-binding region thereof. The immunizedanimal will recognize and respond to the idiotypic determinants of theimmunizing antibody and produce an anti-Id antibody. The anti-Idantibody can also be used as an “immunogen” to induce an immune responsein yet another animal, producing a so-called anti-anti-Id antibody. Theanti-anti-Id can be epitopically identical to the original antibodywhich induced the anti-Id. Thus, by using antibodies to the idiotypicdeterminants of a mAb, it is possible to identify other clonesexpressing antibodies of identical specificity.

Accordingly, monoclonal antibodies generated against CPAA according tothe present invention can be used to induce anti-Id antibodies insuitable animals, such as BALB/c mice. Spleen cells from such immunizedmice can be used to produce anti-Id hybridomas secreting anti-Id mAbs.Further, the anti-Id mAbs can be coupled to a carrier such as keyholelimpet hemocyanin (KLH) and used to immunize additional BALB/c mice.Sera from these mice will contain anti-anti-Id antibodies that have thebinding properties of the original mAb specific for a CPAA epitope.

Idiotypes, Anti-Idiotypes

Additionally, antibodies against CPAA, its analogs, portions, fragments,peptides or derivatives thereof may be used to induce anti-Id antibodiesin suitable animals, such as BALB/c mice. Spleen cells from suchimmunized mice are used to produce anti-Id hybridomas secreting anti-Idmonoclonal antibodies. Further, the anti-Id antibodies can be coupled toa carrier such as keyhole limpet hemocyanin (KLH) and used to immunizeadditional BALB/c mice. Sera from these mice will contain anti-anti-Idantibodies that have the binding properties of the original monoclonalantibody specific for an epitope of CPAA, or analogs, fragments andderivatives thereof. The anti-Id antibodies thus have their ownidiotypic epitopes, or “idiotopes” structurally similar to the epitopebeing evaluated.

An anti-idiotypic (anti-Id) antibody is an antibody that recognizesunique determinants generally associated with the antigen-binding siteof an antibody. An Id antibody can be prepared by immunizing an animalof the same species and genetic type (e.g., mouse strain) as the sourceof the mAb with the mAb to which an anti-Id is being prepared. Theimmunized animal will recognize and respond to the idiotypicdeterminants of the immunizing antibody by producing an antibody tothese idiotypic determinants (the anti-Id antibody). See, e.g., U.S.Pat. No. 4,699,880 and No. 6,835,823. The anti-Id antibody may also beused as an “immunogen” to induce an immune response in yet anotheranimal, producing a so-called anti-anti-Id antibody. The anti-anti-Idmay be epitopically identical to the original mAb which induced theanti-Id. Thus, by using antibodies to the idiotypic determinants of amAb, it is possible to identify other clones expressing antibodies ofidentical specificity.

Structural Analogs of Anti-CPAA Antibodies and Anti-CPAA Peptides

Structural analogs of anti-CPAA antibodies and peptides of the presentinvention are provided by known method steps based on the teaching andguidance presented herein.

Knowledge of the three-dimensional structures of proteins is crucial inunderstanding how they function. The three-dimensional structures ofhundreds of proteins are currently available in protein structuredatabases (in contrast to the thousands of known protein sequences insequence databases). Analysis of these structures shows that they fallinto recognizable classes of motifs. It is thus possible to model athree-dimensional structure of a protein based on the protein's homologyto a related protein of known structure. Many examples are known wheretwo proteins that have relatively low sequence homology, can have verysimilar three dimensional structures or motifs.

In recent years it has become possible to determine the threedimensional structures of proteins of up to about 15 kDa by nuclearmagnetic resonance (NMR). The technique only requires a concentratedsolution of pure protein. No crystals or isomorphous derivatives areneeded. The structures of a number of proteins have been determined bythis method. The details of NMR structure determination are well-knownin the art. See, e.g., Wuthrich, NMR of Proteins & Nucleic Acids (Wiley,N.Y., 1986); Wuthrich, 243 Science 45-50 (1989); Clore et al., 24 Crit.Rev. Bioch. Molec. Biol. 479-564 (1989); Cooke et al., 8 Bioassays 52-56(1988).

In applying this approach, a variety of ¹H NMR 2D data sets arecollected for anti-CPAA antibodies and/or anti-CPAA peptides of thepresent invention. These are of two main types. One type, COSY(Correlated Spectroscopy) identifies proton resonances that are linkedby chemical bonds. These spectra provide information on protons that arelinked by three or less covalent bonds. NOESY (nuclear Overhauserenhancement spectroscopy) identifies protons which are close in space(less than 0.5 nm). Following assignment of the complete spin system,the secondary structure is defined by NOESY. Cross peaks (nuclearOverhauser effects or NOE's) are found between residues that areadjacent in the primary sequence of the peptide and can be seen forprotons less than 0.5 nm apart. The data gathered from sequential NOE'scombined with amide proton coupling constants and NOE's fromnon-adjacent amino acids that are adjacent to the secondary structure,are used to characterize the secondary structure of the peptides. Asidefrom predicting secondary structure, NOE's indicate the distance thatprotons are in space in both the primary amino acid sequence and thesecondary structures. Tertiary structure predictions are determined,after all the data are considered, by a “best fit” extrapolation.

Types of amino acids are first identified using through-bondconnectivities. Next, specific amino acids are assigned usingthrough-space connectivities to neighboring residues, together with theknown amino acid sequence. Structural information is then tabulated andis of three main kinds: The NOE identifies pairs of protons which areclose in space, coupling constants give information on dihedral anglesand slowly exchanging amide protons give information on the position ofhydrogen bonds. The restraints are used to compute the structure using adistance geometry type of calculation followed by refinement usingrestrained molecular dynamics. The output of these computer programs isa family of structures which are compatible with the experimental data(i.e. the set of pairwise <0.5 nm distance restraints). The better thatthe structure is defined by the data, the better the family ofstructures can be superimposed, (i.e., the better the resolution of thestructure). In the better defined structures using NMR, the position ofmuch of the backbone (i.e. the amide, Ca and carbonyl atoms) and theside chains of those amino acids that lie buried in the core of themolecule can be defined as clearly as in structures obtained bycrystallography. The side chains of amino acid residues exposed on thesurface are frequently less well defined, however. This probablyreflects the fact that these surface residues are more mobile and canhave no fixed position. (In a crystal structure this might be seen asdiffuse electron density).

Thus, according to the present invention, use of NMR spectroscopic datais combined with computer modeling to arrive at structural analogs of atleast portions of anti-CPAA antibodies and peptides based on astructural understanding of the topography. Using this information, oneof ordinary skill in the art will know how to achieve structural analogsof anti-CPAA antibodies or peptides, such as by rationally-based aminoacid substitutions allowing the production of peptides in which the CPAAbinding affinity or avidity is modulated in accordance with therequirements of the expected therapeutic or diagnostic use of themolecule, for example, the achievement of greater specificity for CPAAbinding.

Alternatively, compounds having the structural and chemical featuressuitable as anti-CPAA therapeutics and diagnostics provide structuralanalogs with selective CPAA affinity. Molecular modeling studies of CPAAbinding compounds, such as CPAA receptors, anti-CPAA antibodies, orother CPAA binding molecules, using a program such as MACROMODEL®,INSIGHT®, and DISCOVER® provide such spatial requirements andorientation of the anti-CPAA Abs and/or peptides according to thepresent invention. Such structural analogs of the present invention thusprovide selective qualitative and quantitative anti-CPAA activity invitro, in situ and/or in vivo.

Diagnostic Applications

The present invention also provides the above anti-CPAA antibodies andpeptides for use in diagnostic methods for detecting CPAA in patientsknown to be or suspected of having pancreatic or colon carcinoma. Inanother aspect of the invention, the antibodies may detect molecularmarkers in morphologically normal cells to provide for early detectionscreening of disease-free individuals.

Anti-CPAA antibodies and/or peptides of the present invention are usefulfor immunoassays which detect or quantitate CPAA, or anti-CPAAantibodies, in a sample. An immunoassay for CPAA typically comprisesincubating a clinical or biological sample in the presence of adetectably labeled high affinity (or high avidity) anti-CPAA antibody orpolypeptide of the present invention capable of selectively binding toCPAA, and detecting the labeled peptide or antibody which is bound in asample. Various clinical assay procedures are well known in the art.See, e.g., Immunoassays for the 80's (Voller et al., eds., UniversityPark, 1981). Such samples include tissue biopsy, blood, serum, and fecalsamples, or liquids collected from the colorectal track following enemaor oral laxative solution and subjected to ELISA analysis as describedbelow.

Thus, an anti-CPAA antibody or polypeptide can be fixed tonitrocellulose, or another solid support which is capable ofimmobilizing cells, cell particles or soluble proteins. The support canthen be washed with suitable buffers followed by treatment with thedetectably labeled CPAA-specific peptide or antibody. The solid phasesupport can then be washed with the buffer a second time to removeunbound peptide or antibody. The amount of bound label on the solidsupport can then be detected by known method steps.

“Solid phase support” or “carrier” refers to any support capable ofbinding peptide, antigen, or antibody. Well-known supports or carriers,include glass, polystyrene, polypropylene, polyethylene, polyvinylfluoride (PVDF), dextran, nylon, amylases, natural and modifiedcelluloses, polyacrylamides, agaroses, and magnetite. The nature of thecarrier can be either soluble to some extent or insoluble for thepurposes of the present invention. The support material can havevirtually any possible structural configuration so long as the coupledmolecule is capable of binding to CPAA or an anti-CPAA antibody. Thus,the support configuration can be spherical, as in a bead, orcylindrical, as in the inside surface of a test tube, or the externalsurface of a rod. Alternatively, the surface can be flat, such as asheet, culture dish, test strip, etc. For example, supports may includepolystyrene beads. Those skilled in the art will know many othersuitable carriers for binding antibody, peptide or antigen, or canascertain the same by routine experimentation.

Well known method steps can determine binding activity of a given lot ofanti-CPAA peptide and/or antibody. Those skilled in the art candetermine operative and optimal assay conditions by routineexperimentation.

Detectably labeling a CPAA-specific peptide and/or antibody can beaccomplished by linking to an enzyme for use in an enzyme immunoassay(EIA), or enzyme-linked immunosorbent assay (ELISA). The linked enzymereacts with the exposed substrate to generate a chemical moiety whichcan be detected, for example, by spectrophotometric, fluorometric or byvisual means. Enzymes which can be used to detectably label theCPAA-specific antibodies of the present invention include, but are notlimited to, malate dehydrogenase, staphylococcal nuclease,delta-5-steroid isomerase, yeast alcohol dehydrogenase,alpha-glycerophosphate dehydrogenase, triose phosphate isomerase,horseradish peroxidase, alkaline phosphatase, asparaginase, glucoseoxidase, beta-galactosidase, ribonuclease, urease, catalase,glucose-6-phosphate dehydrogenase, glucoamylase andacetylcholinesterase.

By radioactively labeling the CPAA-specific antibodies, it is possibleto detect CPAA through the use of a radioimmunoassay (RIA). See Work etal., LABORATORY TECHNIQUES & BIOCHEMISTRY IN MOLECULAR BIOLOGY (NorthHolland Publishing Co., N.Y. (1978). The radioactive isotope can bedetected by such means as the use of a gamma counter or a scintillationcounter or by autoradiography. Isotopes which are particularly usefulfor the purpose of the present invention are: ³H, ¹²⁵I, ¹³¹I, ³⁵S, ¹⁴C,and ¹²⁵I.

It is also possible to label the CPAA-specific antibodies with afluorescent compound. When the fluorescent labeled antibody is exposedto light of the proper wave length, its presence can then be detecteddue to fluorescence. Among the most commonly used fluorescent labellingcompounds are fluorescein isothiocyanate, rhodamine, phycoerythrin,phycocyanin, allophycocyanin, o-phthaldehyde and fluorescamine.

The CPAA-specific antibodies can also be detectably labeled usingfluorescence-emitting metals such as ¹²⁵Eu, or others of the lanthanideseries. These metals can be attached to the CPAA-specific antibody usingsuch metal chelating groups as diethylenetriaminepentaacetic acid (DTPA)or ethylenediamine-tetraacetic acid (EDTA).

The CPAA-specific antibodies also can be detectably labeled by couplingto a chemiluminescent compound. The presence of the chemiluminescentlylabeled antibody is then determined by detecting the presence ofluminescence that arises during the course of a chemical reaction.Examples of useful chemiluminescent labeling compounds are luminol,isoluminol, theromatic acridinium ester, imidazole, acridinium salt andoxalate ester.

Likewise, a bioluminescent compound can be used to label theCPAA-specific antibody, portion, fragment, polypeptide, or derivative ofthe present invention. Bioluminescence is a type of chemiluminescencefound in biological systems in which a catalytic protein increases theefficiency of the chemiluminescent reaction. The presence of abioluminescent protein is determined by detecting the presence ofluminescence. Important bioluminescent compounds for purposes oflabeling are luciferin, luciferase and aequorin.

Detection of the CPAA-specific antibody, portion, fragment, polypeptide,or derivative can be accomplished by a scintillation counter, forexample, if the detectable label is a radioactive gamma emitter, or by afluorometer, for example, if the label is a fluorescent material. In thecase of an enzyme label, the detection can be accomplished bycolorometric methods which employ a substrate for the enzyme. Detectioncan also be accomplished by visual comparison of the extent of enzymaticreaction of a substrate in comparison with similarly prepared standards.

For the purposes of the present invention, the CPAA which is detected bythe above assays can be present in a biological sample. Any samplecontaining CPAA can be used. For example, the sample is a biologicalfluid such as, for example, blood, serum, lymph, urine, feces,inflammatory exudate, cerebrospinal fluid, amniotic fluid, a tissueextract or homogenate, and the like. However, the invention is notlimited to assays using only these samples, it being possible for one ofordinary skill in the art to determine suitable conditions which allowthe use of other samples.

In situ detection can be accomplished by removing a histologicalspecimen from a patient, and providing the combination of labeledantibodies of the present invention to such a specimen. The antibody (orfragment) may be provided by applying or by overlaying the labeledantibody (or fragment) to a biological sample. Through the use of such aprocedure, it is possible to determine not only the presence of CPAA butalso the distribution of CPAA in the examined tissue. Using the presentinvention, those of ordinary skill will readily perceive that any of awide variety of histological methods (such as staining procedures) canbe modified in order to achieve such in situ detection.

The antibody, fragment or derivative of the present invention can beadapted for utilization in an immunometric assay, also known as a“two-site” or “sandwich” assay. In a typical immunometric assay, aquantity of unlabeled antibody (or fragment of antibody) is bound to asolid support that is insoluble in the fluid being tested and a quantityof detectably labeled soluble antibody is added to permit detectionand/or quantitation of the ternary complex formed between solid-phaseantibody, antigen, and labeled antibody.

Typical, immunometric assays include “forward” assays in which theantibody bound to the solid phase is first contacted with the samplebeing tested to extract the CPAA from the sample by formation of abinary solid phase antibody-CPAA complex. After a suitable incubationperiod, the solid support is washed to remove the residue of the fluidsample, including unreacted CPAA, if any, and then contacted with thesolution containing a known quantity of labeled antibody (whichfunctions as a “reporter molecule”). After a second incubation period topermit the labeled antibody to complex with the CPAA bound to the solidsupport through the unlabeled antibody, the solid support is washed asecond time to remove the unreacted labeled antibody. This type offorward sandwich assay can be a simple “yes/no” assay to determinewhether CPAA is present or can be made quantitative by comparing themeasure of labeled antibody with that obtained for a standard samplecontaining known quantities of CPAA. Such “two-site” or “sandwich”assays are described by Wide, Radioimmune Assay Methods, 199-206(Kirkham, ed., Livingstone, Edinburgh, 1970).

Other type of “sandwich” assays, which can also be useful with CPAA, arethe so-called “simultaneous” and “reverse” assays. A simultaneous assayinvolves a single incubation step wherein the antibody bound to thesolid support and labeled antibody are both added to the sample beingtested at the same time. After the incubation is completed, the solidsupport is washed to remove the residue of fluid sample and uncomplexedlabeled antibody. The presence of labeled antibody associated with thesolid support is then determined as it would be in a conventional“forward” sandwich assay.

In the “reverse” assay, stepwise addition first of a solution of labeledantibody to the fluid sample followed by the addition of unlabeledantibody bound to a solid support after a suitable incubation period, isutilized. After a second incubation, the solid phase is washed inconventional fashion to free it of the residue of the sample beingtested and the solution of unreacted labeled antibody. The determinationof labeled antibody associated with a solid support is then determinedas in the “simultaneous” and “forward” assays. In one embodiment, acombination of antibodies of the present invention specific for separateepitopes can be used to construct a sensitive three-siteimmunoradiometric assay.

Additionally, the exemplary antibodies can be utilized for T-celltyping, for isolating specific CPAA-bearing cells or fragments, forvaccine preparation, or the like. The antibodies may be used toquantitatively or qualitatively detect the CPAA in a sample or to detectpresence of cells that express the CPAA. This can be accomplished byimmunofluorescence techniques employing a fluorescently labeled antibody(see below) coupled with fluorescence microscopy, flow cytometric, orfluorometric detection. For diagnostic purposes, the antibodies mayeither be labeled or unlabeled. Unlabeled antibodies can be used incombination with other labeled antibodies (second antibodies) that arereactive with the humanized antibody, such as antibodies specific forhuman immunoglobulin constant regions. Alternatively, the antibodies canbe directly labeled. A wide variety of labels may be employed, such asradionuclides, fluors, enzymes, enzyme substrates, enzyme cofactors,enzyme inhibitors, ligands (particularly haptens), etc. Numerous typesof immunoassays, such as those discussed previously are available andare well known to those skilled in the art.

The antibodies useful in the present invention may be employedhistologically, as in immunofluorescence or immunoelectron microscopy,for in situ detection of the CPAA of the present invention. In situdetection may be accomplished by removing a histological specimen from apatient, and providing the labeled antibody of the present invention tosuch a specimen. The antibody (or fragment) may be provided by applyingor by overlaying the labeled antibody (or fragment) to a biologicalsample. Through the use of such a procedure, it is possible to determinenot only the presence of the CPAA but also its distribution on theexamined tissue. Using the present invention, those of ordinary skillwill readily perceive that any of wide variety of histological methods(such as staining procedures) can be modified in order to achieve suchin situ detection.

Importantly, the antibodies of the present invention may be helpful indiagnosing the invasiveness of certain types of colorectal andpancreatic cancer. More specifically, the antibody of the presentinvention may identify CPAA present in patients with slow cancers thatgrow over several years as opposed to aggressive cancers that progressmuch faster. Thus, the antibody of the present invention may provide animportant immunohistochemistry tool.

The antibodies of the present invention may be used on antibody arrays,highly suitable for measuring gene expression profiles includingpost-translational modification and also useful for detecting smallermolecules such as peptide hormones and carbohydrates. Several approacheshave recently been employed to determine the suitability and efficacy ofantibody arrays. In some instances, phage-displayed antibodies have beenused in preparing the arrays, and detection and analysis is done bySELDI (surface-enhanced laser desorption/ionization), or in ahigh-throughput format by filter-based enzyme-linked immunosorbent assay(ELISA). Other examples of detection systems include fluorescent tagsand nanoelectrodes, and for smaller arrays, surface plasmon resonanceand MALDI-TOF (matrix-assisted laser desorption ionization-time offlight) mass spectrometry. Proteome analysis can also be performed byfirst generating an array of bound antigens followed by antibody captureand detection with an affinity ligand such as Protein L or Protein Abound to a detection probe.

A third approach involves high-density gridding of bacteria containingantibody genes onto a filter followed by interaction with another filtercontaining an affinity ligand or the antigen attached with a detectionprobe such as ELISA. This method eliminates the need for liquidhandling, and parallel screens of tens of thousands of antibodiesagainst multiple antigens can be performed to identify ultimatelyproteins that are differentially expressed. A final method involves thepossibility of synthesizing antibodies directly on the chip usingcombinatorial chemistry. Current technology, however, somewhat strainedat synthesizing even the antigen-binding antibody domains that consistsof a minimum of 120 aminoacids, unless presynthesized polypeptidebuilding blocks are used to create an antibody framework followed by theaddition of individual amino acids.

Screening methods for determining anti-CPAA activities are also providedfor in the present invention. Specifically, as described further inExample 6, the antibody of the present invention is associated withantibody-dependent cellular cytotoxicity (ADCC) activity. Anti-CPAAcompounds that can be selected from the group consisting of antibodies,or fragments or portions thereof, peptides, peptido mimetic compounds ororgano mimetic compounds that trigger death of CPAA-bearing cells invitro, in situ or in vivo are encompassed by the present invention.Screening methods which can be used to determine ADCC activity of ananti-CPAA compound can include in vitro or in vivo assays. Such in vitroassays can include a CPAA cytotoxicity assay, such as aradioimmunoassay, which determines a decrease in cell death by contactwith CPAA, such as chimpanzee or human CPAA in isolated or recombinantform, wherein the concurrent presence of a CPAA neutralizing compoundreduces the degree or rate of cell death.

Diagnostic Kits

Kits can also be supplied for use with the subject antibodies in theprotection against or detection of a cellular activity or for thepresence of a selected antigen. Thus, an antibody of the presentinvention may be provided, usually in a lyophilized form in a container,either alone or in conjunction with additional antibodies specific forthe desired cell type. The antibodies, which may be conjugated to alabel or toxin, or unconjugated, are included in the kits with buffers,such as Tris, phosphate, carbonate, etc., stabilizers, biocides, inertproteins, e.g., serum albumin, or the like. Generally, these materialswill be present in less than 5% wt. based on the amount of activeantibody, and usually present in total amount of at least about 0.001%wt. based again on the antibody concentration. Frequently, it will bedesirable to include an inert extender or excipient to dilute the activeingredients, where the excipient may be present in from about 1% to 99%wt. of the total composition. Where a second antibody capable of bindingto the primary antibody is employed in an assay, this will usually bepresent in a separate vial. The second antibody is typically conjugatedto a label and formulated in an analogous manner with the antibodyformulations described above. The kit will generally also include a setof instructions for use.

Pharmaceutical Applications

The anti-CPAA antibodies or peptides of the present invention can beused for example in the treatment of carcinomas and related conditions.More specifically, the invention further provides for a pharmaceuticalcomposition comprising a pharmaceutically acceptable carrier or diluentand, as active ingredient, an antibody or peptide according to theinvention. The delivery component of the immunotoxin is a humanizedantibody according to the present invention. Intact immunoglobulins ortheir binding fragments, such as Fab, are also envisioned. Typically,the antibodies in the immunotoxins will be of the human IgA, IgM or IgGisotype, but other mammalian constant regions may be utilized asdesired. The composition may also comprise an immunotoxin according tothe invention. The humanized antibody, immunotoxin and pharmaceuticalcompositions thereof of this invention are useful for parenteraladministration, i.e., subcutaneously, intramuscularly or intravenously.

Anti-CPAA antibodies and/or peptides of the present invention can beadministered either as individual therapeutic agents or in combinationwith other therapeutic agents. They can be administered alone, but aregenerally administered with a pharmaceutical carrier selected on thebasis of the chosen route of administration and standard pharmaceuticalpractice.

For parenteral administration, anti-CPAA antibodies or peptides can beformulated as a solution, suspension, emulsion or lyophilized powder inassociation with a pharmaceutically acceptable parenteral vehicle. Forexample the vehicle may be a solution of the antibody or a cocktailthereof dissolved in an acceptable carrier, such as an aqueous carriersuch vehicles are water, saline, Ringer's solution, dextrose solution,or 5% human serum albumin, 0.4% saline, 0.3% glycine and the like.Liposomes and nonaqueous vehicles such as fixed oils can also be used.These solutions are sterile and generally free of particulate matter.These compositions may be sterilized by conventional, well knownsterilization techniques. The compositions may contain pharmaceuticallyacceptable auxiliary substances as required to approximate physiologicalconditions such as pH adjusting and buffering agents, toxicityadjustment agents and the like, for example sodium acetate, sodiumchloride, potassium chloride, calcium chloride, sodium lactate, etc. Theconcentration of antibody in these formulations can vary widely, forexample from less than about 0.5%, usually at or at least about 1% to asmuch as 15% or 20% by weight and will be selected primarily based onfluid volumes, viscosities, etc., in accordance with the particular modeof administration selected. The vehicle or lyophilized powder cancontain additives that maintain isotonicity (e.g., sodium chloride,mannitol) and chemical stability (e.g., buffers and preservatives). Theformulation is sterilized by commonly used techniques.

Thus, a typical pharmaceutical composition for intramuscular injectioncould be made up to contain 1 ml sterile buffered water, and 50 mg ofantibody. A typical composition for intravenous infusion could be madeup to contain 250 ml of sterile Ringer's solution, and 150 mg ofantibody. Actual methods for preparing parenterally administrablecompositions will be known or apparent to those skilled in the art andare described in more detail in, for example, Remington's PharmaceuticalScience (15th ed., Mack Pub. Co., Easton, Pa., 1980).

The antibodies of this invention can be lyophilized for storage andreconstituted in a suitable carrier prior to use. This technique hasbeen shown to be effective with conventional immune globulins. Anysuitable lyophilization and reconstitution techniques can be employed.It will be appreciated by those skilled in the art that lyophilizationand reconstitution can lead to varying degrees of antibody activity loss(e.g., with conventional immune globulins, IgM antibodies tend to havegreater activity loss than IgG antibodies) and that use levels may haveto be adjusted to compensate.

The compositions containing the present human-like antibodies or acocktail thereof can be administered for prevention of recurrence and/ortherapeutic treatments for existing disease. Suitable pharmaceuticalcarriers are described in the most recent edition of Remington'sPharmaceutical Sciences, a standard reference text in this field of art.For example, a parenteral composition suitable for administration byinjection is prepared by dissolving 1.5% by weight of active ingredientin 0.9% sodium chloride solution. Anti-CPAA peptides and/or antibodiesof this invention can be adapted for therapeutic efficacy by virtue oftheir ability to mediate antibody-dependent cellular cytotoxicity(ADCC), and/or apoptosis, and/or complement-dependent cytotoxicity (CDC)against cells having CPAA associated with their surface. For theseactivities, either an endogenous source or an exogenous source ofeffector cells (for ADCC) or complement components (for CDC) can beutilized.

In therapeutic application, compositions are administered to a patientalready suffering from a disease, in an amount sufficient to cure or atleast partially arrest or alleviate the disease and its complications.An amount adequate to accomplish this is defined as a “therapeuticallyeffective dose.” Amounts effective for this use will depend upon theseverity of the malignancy and the general state of the patient's ownimmune system, but generally range from about 1 mg to about 200 mg ofantibody per dose, with dosages of from 5 mg to 25 mg per patient beingmore commonly used. It must be kept in mind that the materials of theinvention may generally be employed in serious disease states, oftenlife-threatening or potentially life-threatening situations. In suchcases, in view of the minimization of extraneous substances and thelower probability of “foreign substance” rejections which are achievedby the present human-like antibodies of this invention, it is possibleand may be felt desirable by the treating physician to administersubstantial excesses of these antibodies.

The dosage administered will, of course, vary depending upon knownfactors such as the pharmacodynamic characteristics of the particularagent, and its mode and route of administration; age, health, and weightof the recipient; nature and extent of symptoms, kind of concurrenttreatment, frequency of treatment, and the effect desired. Usually adaily, weekly, or biweekly dosage of active ingredient can be about 100mg/m² to 250 mg/m² of body weight delivered over a 4 hour to 6 hourperiod.

As a non-limiting example, treatment of CPAA-related pathologies humansor animals can be provided as a daily, weekly, or biweekly dosage ofanti-CPAA peptides, monoclonal chimeric and/or murine antibodies of thepresent invention in a dosage range from 0.1 mg/kg to 100 mg/kg, perday, weekly, or biweekly.

Example antibodies for human therapeutic use are high affinity (thesemay also be high avidity) murine and chimeric antibodies, and fragments,regions and derivatives having potent in vivo anti-CPAA activity,according to the present invention.

Dosage forms (composition) suitable for internal administrationgenerally contain from about 0.1 milligram to about 500 milligrams ofactive ingredient per unit. In these pharmaceutical compositions theactive ingredient will ordinarily be present in an amount of about0.5-95% by weight based on the total weight of the composition.

Single or multiple administrations of the compositions can be carriedout with dose levels and pattern being selected by the treatingphysician. In any event, the pharmaceutical formulations should providea quantity of the antibody(ies) of this invention sufficient toeffectively treat the patient.

The antibodies can also be used as separately administered compositionsgiven in conjunction with chemotherapeutic or immunosuppressive agents.Typically, the agents will include cyclosporin A or a purine analog(e.g., methotrexate, 6-mercaptopurine, or the like), but numerousadditional agents (e.g., cyclophosphamide, prednisone, etc.) well-knownto those skilled in the art may also be utilized.

An antibody of the present invention may form part of an immunotoxin.Immunotoxins are characterized by two components and are useful forkilling selected cells in vitro or in vivo. One component is a cytotoxicagent which is usually fatal to a cell when attached or absorbed. Thesecond component, known as the “delivery vehicle”, provides a means fordelivering the toxic agent to a particular cell type, such as cellscomprising a carcinoma. The two components are commonly chemicallybonded together by any of a variety of well-known chemical procedures.For example, when the cytotoxic agent is a protein and the secondcomponent is an intact immunoglobulin, the linkage may be by way ofheterobifunctional cross-linkers, e.g., SPDP, carbodiimide,glutaraldehyde, or the like. Production of various immunotoxins iswell-known with the art, and can be found, for example in Thorpe et al.,“Monoclonal Antibody-Toxin Conjugates: Aiming the Magic Bullet,”Monoclonal Antibodies in Clinical Medicine, 168-190 (Academic Press,1982).

A variety of cytotoxic agents are suitable for use in immunotoxins.Cytotoxic drugs interfere with critical cellular processes includingDNA, RNA, and protein synthesis. Cytotoxic agents can includeradionuclides, such as include ²¹²Bi, ¹³¹I, ¹⁸⁸Re, and ⁹⁰Y; a number ofchemotherapeutic drugs, such as vindesine, methotrexate, adriamycin, andcisplatin; and cytotoxic proteins such as ribosomal inhibiting proteinslike pokeweed antiviral protein, Pseudomonas exotoxin A, ricin,diphtheria toxin, ricin A chain, etc., or an agent active at the cellsurface, such as the phospholipase enzymes (e.g., phospholipase C). See,generally, Olsnes & Phil “Chimeric Toxins,” 25 Pharmac. Ther., 335-81(1982); “Monoclonal Antibodies for Cancer Detection and Therapy,”159-79, 224-66 (Baldwin & Byers eds., Academic Press, 1985).

The antibodies or peptides and derivatives can be used therapeuticallyas immunoconjugates. See Dillman, 111 Ann. Int. Med. 592-603 (1989).Such antibodies or polypeptides can be coupled to cytotoxic proteins,including, but not limited to ricin-A, Pseudomonas toxin and Diphtheriatoxin. Toxins conjugated to antibodies or other ligands or peptides arewell known in the art. See, e.g., Olsnes et al., 10 Immunol. Today291-95 (1989). Plant and bacterial toxins typically kill cells bydisrupting the protein synthetic machinery. Cytotoxic drugs that can beconjugated to anti-CPAA peptides and/or antibodies and subsequently usedfor in vivo therapy include, but are not limited to, daunorubicin,doxorubicin, methotrexate, and Mitomycin C. For a description of theseclasses of drugs which are well known in the art, and their mechanismsof action, see Goodman & Gilman's THE PHARMACOLOGICAL BASIS OFTHERAPEUTICS (8th Ed., Macmillan Publishing Co., 1990).

Additionally, the antibody of the present invention may be delivered incombination with chemotherapeutic agents such as oxaliplatin,irinotecan, topotecan, leucovorin, carmustine, vincristine,fluorouracil, streptozocin, and gemcitabine. Combinations of otherantibodies and such compounds have been used in advanced colorectalcancer patients. See, e.g., U.S. Patent Appl. Pub. No. 2002/0187144.

Anti-CPAA antibodies and/or peptides of this invention can beadvantageously utilized in combination with other monoclonal or murineand chimeric antibodies, fragments and regions, or with lymphokines orhemopoietic growth factors, etc., which serve to increase the number oractivity of effector cells which interact with the antibodies. Forexample, the antibody of the present invention may be co-administeredwith human monoclonal antibodies reactive with other markers on cellsresponsible for the disease. For example, suitable T-cell markers caninclude those grouped into the so-called “Clusters of Differentiation”as named by the First International Leukocyte Differentiation Workshop,Leukocyte Typing (Bernard et al., eds., Springer-Verlag, N.Y., 1984).

Cancer Vaccine

Another aspect of the present invention provides for a cancer vaccine.By “vaccine” is meant an agent used to stimulate the immune system of aliving organism. In this regard, the immune response may provide forprophylaxis or may provide for a positive effect in a diseased organismby, for example, alleviating an existing condition. Specifically, acancer vaccine is meant to therapeutically treat existing malignancyand/or to prevent the progression or metastasis of an existingmalignancy.

That specific active immunotherapy can be achieved usingtumor-associated antigens is widely known. Indeed, the initial,roughly-purified antigenic preparations used to derive the monoclonalantibody that has allowed the further invention presented herein wasshown to provide for protective immunity in humans. Hollinshead et al.,1985. At that time, patients had undergone tumor resection and were thenvaccinated with antigenic material derived from tumor membranes in theamount of 200 μg, 300 μg, or 500 μg in 0.2 ml dispersions mixed with anadditional 0.2 ml Freund's adjuvant. Dosages of 300 μg given monthly forthree months were shown to be safe.

With the recombinant antibodies described herein, it is now possible todefine a highly purified antigen or epitope peptides of CPAA that isfurther suitable for a vaccine against these cancers. For example, NPC-1may be used to bind to tissue or cell samples from which the CPAAprotein and its corresponding amino acid sequence may be identified byany number of known techniques. The epitope may be mapped further, andthe molecular nature determined with exquisite detail. See, e.g,Baerga-Oritz et sl., “Epitope mapping of a monoclonal antibody againsthuman thrombin by H/D-exchange mass spectropmetry reveals selection of adivers sequence in a highly conserved sequence,” 11 Protein Sci. 1300-08(2002); Jemmerson, & Paterson, “Mapping antigenic sites on proteins:implications for the design of synthetic vaccines,” 4 BioTechniques18-31 (1986).

An alternative technique to identify effective antigenic peptidesentails using the NPC-1 antibody or peptide to screen an expressionlibrary (such as a phage display library) for mimetic proteins, ormimotopes, that are recognized by the antibody. This technique has beenused to identify antigenic peptides that have raised protective immuneresponses in vivo. See Beenhouwer et al., 169 J. Immunol. 6992-99(2002); see also U.S. Pat. No. 5,837,550; Visvanathan et al., 48Arthritis & Rheumatism, 737-45 (2003); Sato et al., 371 Biochem. J.603-08 (2003). Note that this technique has been used to identifyprotein mimetics of carbohydrate and glycoprotein antigens, the proteinversions found to be more immunogenic than the natural carbohydratecounterparts. Indeed, mimetics may be isolated that are advantageousover known antigens because of factors including production capacity,safety, half-life, or other issues.

The CPAA immunogenic protein may be prepared and delivered, for example,as either a subcutaneous or a mucosal vaccine alone, or associated withan adjuvant or carrier or as part of an adjuvant or protein conjugate.Delivery by liposomes microparticles, virus-like particles, DNAvaccines, live recombinant vectors such as Salmonella typhimurium, andpossibly ISCOMs are envisioned. All of these systems are well-known bythose of ordinary skill in the art, and may be practiced without undueexperimentation. See, e.g., Michalek et al., “Antigen Delivery SystemsI: Nonliving Microparticles, Liposome, and Immune Stimulating Complexes(ISCOMs),” in MUCOSAL IMMUNOLOGY (Mestecky et al., eds., Elsevier,2005).

Additionally, the CPAA peptide may be genetically or chemicallyconjugated to a toxoid carrier, such as cholera, entero, or ricintoxoid. See, e.g., U.S. Pat. No. 6,846,488. Another advantageous proteincarrier derived from bacterium is the PorB protein carrier. See e.g.,U.S. Pat. No. 6,613,336. Another promising protein-based mucosaladjuvant is the flagellin protein from S. typhimurium. In an embodimentof the invention, the CPAA protein is co-administered with the flagellinprotein (FljB) via, for example, the mucosal intranasal route. Anadvantageous protein platform comprising duck hepatitis core antigen isalso presented in U.S. Patent Appl. Pub. No. 2004/0219164.

The CPAA of the present invention may also be delivered as a DNA vaccinefor in vivo expression of the immunogenic construct. For example,cationic microparticles may be used to deliver the DNA expressioncassette in intranasal vaccination. Such systems have induced an immuneresponse following, for example, intranasal delivery of vaccinecomprising DNA encoding the HIV-1 gag protein. Michalek et al., 2005. Inan embodiment of the present invention, the CPAA immunogenic peptide isdelivered via a DNA expression cassette which is subsequently expressedin vivo.

Additionally, the immunogenic preparation may be used to “charge” donorderived dendritic cells ex vivo, which are then returned to the patientwhere they home to the lymphoid organs and mount an effective immuneresponse. See, e.g., Baar, J. “Clinical applications of dendritic cellcancer vaccines,” 4 (2) Oncologist, 140-44 (1999). This vaccine approachis currently in human trials for treating, for example, melanoma. Moreinformation can be found at the Dartmouth-Hitchcock Medical Centerwebsite, under Clinical Trials. Alternatively, a DNA vaccine asdescribed above may be delivered via skin patch to the cells ofLangerhans, which then mature to dendritic cells and home to thelypmphoid organs. U.S. Pat. No. 6,420,176.

Delivery of the immunogenic compositions of the present invention may beby parenteral, subcutaneous, or intramuscular injection, intravenousinjection, intestinal, intradermal, intubation, or nasal, oral or rectalvaccination. The vaccine may also be delivered topically, includingintranasal, upon the palatine tonsil, or delivery to the salivaryglands. Administration of a vaccine contemplated by the presentinvention to the patient may be by any known or standard techniques.

The invention will now be described further by non-limiting examples.

Examples Example 1. Preparation of Pancreatic and ColorectalCarcinoma-Associated Antigen (CPAA) from Human Tumor Specimens

An immunogenic tumor associated antigen preparation was obtained frompooled colorectal carcinoma membranes according to the method describedby Hollinshead et al., 56 Cancer 480 (1985); U.S. Pat. No. 5,688,657.This antigenic material was purified to the extent that the membranefractions were free of HL-A antigens and were separated from much of thenon-immunogenic glycoprotein fractions.

Tumor cell suspensions in saline were prepared from fresh operating roomspecimens. Single cell suspensions, obtained by mincing solid tumors,were centrifuged for 10 minutes at 400× gravity and the supernatant wasretained. The cell pellet was resuspended in phosphate buffered saline(PBS) and re-centrifuged. The membrane material was examined by electronmicroscopy to assure that only membrane material (and no intact cells)was present, and the protein content was measured by the Lowry method.The membrane material was next subjected to sequential low frequencysonication and resuspended as a soluble pool of membrane proteins. Thesoluble sonicates were separated by gel filtration on Sephadex-6200.Fractions of 2 milliliters (ml) were collected and the absorbanceprofile at 220 and 280 nanometers (nm) was recorded. Fractionscomprising individual protein peaks were pooled, and the pools wereconcentrated by Diaflo ultrafiltration. Sephadex-G200 fractions IB andIIA, as defined by Hollinshead et al., 1985, were further purified bygradient polyacrylamide gel electrophoresis (PAGE). The fractions weretested for their ability to elicit positive delayed cutaneoushypersensitivity reactions in patients with colorectal carcinoma. Thosefractions with immunogenic activity were said to contain colorectalcarcinoma-associated antigens and were employed as immunogens andscreening agents in the preparation of monoclonal antibodies.

By gradient PAGE, a double-banded antigen distinct from that ofcarcinoembryonic antigen (Gold et al., 122 J. Exp. Med. 467-81 (1965);Hollinshead et al., 1985) was identified and isolated. The bandscomprising this antigen migrated 6.3 cm and 6.6 cm distant from trackingdye. Biochemical analysis of the antigen indicated that this protein wasa glycoprotein. The molecular weight of the antigen was estimated basedon the electrophoretic mobility of transferrin (6.4-6.5 cm) which has amolecular weight of 76.5 kDa.

Example 2. Immunization and Preparation of Hybridomas

Monoclonal antibodies against human colorectal and pancreaticcarcinoma-associated antigens (CPAA) were obtained by the production andcloning of hybrids resulting from the fusion of mouse myeloma cellsSp2/0-Ag14 with spleen cells from BALB/c mice which had been immunizedwith the CPAA described above. Hybrid clones were established andreacted strongly with the CPAA and with two colon carcinoma cell lines(SW480 and SW620) when assayed by ELISA.

A. Immunization and Cell Fusion:

BALB/c mice were immunized by intraperitoneal injection of 50 μg of theCPAA described above emulsified in complete Freund's adjuvant, asdescribed by Hollinshead in clinical trials (Hollinshead et al., 1985).Ten days later, the mice received an intravenous booster injection ofthe same amount of CPAA in saline. Mice were sacrificed three days laterand a single cell splenocyte suspension was prepared. Cell fusion wasperformed by incubating 5e7 mouse spleen cells with 10e7 sP2/0-Ag14myeloma cells in 40% polyethylene glycol (MW=1500).

B. Screening of Hybrid Clones:

An enzyme-linked immunosorbent assay (ELISA), described by Tsang et al.,77 JNCI 1175 (1986), was used for the detection of hybridoma clonesproducing antibodies specific for the CPAA. CPAA (100 ng/well) wasimmobilized on polystyrene microplates. Antibodies present in the testsupernatants were allowed to bind to the immobilized antigens for onehour. The presence of the bound murine mAbs was detected withperoxidase-conjugated secondary antibodies, specific for mouseimmunoglobulins. Wells were washed and then the chromogenic substratefor peroxidase, O-phenyldiamine was added. Wells showing color reactionsyielding absorbances greater or equal to 0.500 units were scored aspositive. Negative controls gave values of 0.01 to 0.09 absorbanceunits. Hybridoma wells scoring as positive by ELISA were selected forexpansion and repeating the cell cloning procedure by the limitingdilution cloning method. Selection of positive mAb producing hybridomacells was determined by ELISA. Positive monoclonal cells were expandedin culture and aliquots of the cells were frozen under liquid nitrogenfor long term storage.

Example 3. Isotype of NPC-1 Monoclonal Antibody

Murine immunoglobulins are expressed from separate genes that encode theheavy chain (55 kD) and the light chain (25-29 kD). There are four heavychains of the IgG subclass (IgG1, IgG2a, IgG2b, IgG3) and two lightchains (Kappa, Lambda) that can rearrange to yield the repertoire ofmurine immunoglobulins.

The isotype of the NPC-1 mAb was determined using a commercial mouseisotyping kit (catalog no. RPN29, GE Healthcare (formerly AmershamBiosciences). The assay involves incubating the test hybridomasupernatant with the isotyping stick, which includes pre-blottedanti-mouse Ig specific antibodies in marked areas of the stick.Detection of the test material is by horseradish peroxidase-conjugatedanti-mouse Ig antibody and development with the peroxidase substrate,OPD. A positive color reaction indicated the heavy chain and the lightchain expressed by the hybridoma, thus describing the Ig isotype of themAb. The NPC-1 mAb was determined to be an IgG1 heavy chain and a Kappalight chain.

Example 4. DNA Sequence and Uniqueness of the NPC-1 Antibody

The linear amino acid sequence of a mAb identified NPC-1 as unique incomparison to the all the sequences of which the Applicants were aware.The linear amino acid sequence was be determined by first determiningthe linear sequence of the DNA that encodes the polypeptide molecule.The DNA sequence encoding the NPC-1 mAb was determined and the openreading frame was translated into the amino acid sequence using theuniversal mammalian codon usage table, thus describing the linearsequence identity of the NPC-1 molecule.

Oligonucleotide primers used for the murine IgG1 heavy chain reversetranscription, PCR, and sequencing reactions derived from the Constant-1region of the heavy chain described in GenBank (AB097849). Primers usedfor the murine kappa light chain reverse transcription, PCR, andsequencing reactions derived from the Constant region of the light chaindescribed in GenBank (AB097848).

A. Isolation of the Nucleic Acid of NPC-1

RNA was isolated from the NPC-1 producing hybridoma cells using thecommercially available RNeasy-Midi kit (catalog no. 74104, Qiagen) asinstructed by the manufacturers. Four million hybridoma cells werecentrifuged in a conical tube, and the cells were lysed to release thenuclear and cytosolic nucleic acids including the RNA. The RNA was thenpurified from the lysate using the RNeasy spin columns. The RNA was theneluted with water and analyzed for yield and purity by absorbance at 260nm and 280 nm using a spectrophotometer. The RNA was stored at −80° C.

B. Preparation of the cDNA

The RNA (2 μg) was first reverse-transcribed to cDNA using adeoxynucleotide triphosphate dNTP mixture (dATP, dCTP, dGTP, dTTP), cDNAsynthesis buffer, RNase inhibitor, reverse transcriptase enzyme, andoligonucleotide primers specific for the heavy (IgG1) and light (Kappa)chains of the NPC-1 isotype. The reagents were provided in a 5′/3′ RACEKit (catalog no. 03-353, Roche Applied Sciences). The reactionprogressed for 60 minutes at 55° C., followed by 5 minutes at 85° C. ThecDNA was then purified by spin column (catalog no. 1-732-668, RocheApplied Sciences) and subjected to polyadenylation using dATP andterminal transferase for 30 minutes at 37° C. The polyadenylationreagents were also provided in the 5′/3′ RACE kit (Roche AppliedSciences). Finally, the target DNA (mouse IgG1 heavy chain and Kappalight chain) were amplified for sequencing by the polymerase chainreaction (PCR) as defined by the following reaction: polyA-tailed cDNAtemplate, oligo dT anchor primer, dNTP mixture, reaction buffer, ExpandHigh Fidelity Polymerase enzyme, and the specific oligonucleotides foreither the IgG heavy chain or the Kappa light chain. Reagents for thePCR were obtained commercially (catalog no. 1-732-641, Roche AppliedSciences). The mixture was subjected to 94° C. for 2 minutes, followedby 10 cycles of: 15 seconds at 94° C., 30 seconds at 55° C., 40 secondsat 72° C., which was followed by twenty-five cycles of: 15 seconds at94° C., 30 seconds at 55° C., 60 seconds at 72° C. Following this, thereactions were incubated for 7 minutes at 72° C. and then cooled to 4°C. The amplified heavy and light chain DNA fragments were then gelpurified on a 1% agarose gel. The target DNA bands were excised from thegel and then purified from the agarose using QIAquick gel extraction kit(catalog no. 28704, Qiagen).

C. DNA Sequencing and Analysis

Amplified target DNA was subjected to sequencing reactions using thedideoxynucleotide incorporation method. The entire sequence of the IgG1heavy chain and Kappa light chain were determined using the previousmentioned primers and reagents from Applied Biosystems (BigDyeTerminator V1.1 Cycle Sequencing kit, Part 4346776). Automatedsequencing analysis was performed using the ABI-377 and ABI-310 DNAsequencers. The DNA sequence was translated in three reading frames andthe frame without stop codons and that aligned homologously with othermurine heavy and light chains was determined to be the genuine readingframe. The cDNA sequence for the light chain is presented in FIG. 2, andthe corresponding amino acid sequence is presented in FIG. 3. The cDNAsequence of the heavy chain is presented in FIGS. 4A-4B, and thecorresponding amino acid sequence is presented in FIGS. 5A-5B. Thevariable, constant, and CDR regions of the light chain are presented inFIG. 6, and the variable, constant, and CDR regions of the heavy chainare presented in FIG. 7

The DNA sequence was used as the query sequence to search the NationalCenter for Biotechnology Information (NCBI) database (All GenBank+RefSeqNucleotides+EMBL+DDBJ+PDB sequences). The BLAST search returned up to 15database entries with nucleotide sequence similarity to the querysequence of NPC-1. None of the DNA sequences were identical to the NPC-1DNA sequence, demonstrating the uniqueness of the NPC-1 monoclonalantibody described herein.

Example 5. Specific Cell Binding of NPC-1

The NPC-1 mAb produced by the hybridoma was purified by affinitychromatography using protein L-agarose matrix. The purified NPC-1 wascharacterized by indirect immunofluorescence as well-known in the artusing various tumor cells as identified in Table 1, below. All of thetumor cell lines were obtained from the ATCC. Cells were incubated withpurified NPC-1 diluted in phosphate buffered saline (PBS) for 1 hour at4° C. The cells were washed and incubated with a fluorescein-labelledgoat anti-mouse immunoglobulin antibody. The cells were then washedthree times with PBS and examined by flow cytometry using aBecton-Dickinson FACScalibur and CellQuest analysis software. Theresults appear in Table 1 (FACS data). The data demonstrate the specificbinding of NPC-1 to colorectal and pancreatic tumor cell lines, but notto ovarian or breast tumor cell lines.

TABLE 1 Cancer cell types recognized by NPC-1 % Cell Staining Tumor CellLine Unstained Isotype Control NPC-1 GEO Colorectal 1.36 0.78 86.87LS174T Colorectal 1.31 0.93 57.04 CFPAC-1 Pancreatic 1.24 0.44 54.65OVCAR-3 Ovarian 0.21 0.19 0.19 MCF-7 Breast 1.23 0.94 0.19Flow cytometry antibody binding data with various cultured tumor celllines. Cells stained with 2.5 μg NPC-1 per 100,000 cells.

Example 6. ADCC Activity of NPC-1 Demonstrating Anti-Tumor Cytotoxicity

A therapeutically useful monoclonal antibody, specific for animmunogenic tumor antigen, may have one or more of the followingproperties: (a) high tumor tissue specificity; (b) absence ofcross-reactivity to normal human tissue; and (c) a biological activityassociated with destruction of tumors, such as antibody-dependentcellular cytotoxicity (ADCC). The ADCC activity of NPC-1 was tested oncolon LS174T and pancreatic CFPAC-1 carcinoma lines as target cells. Theovarian cell line, OVCAR-3, served as a specificity control. ADCC wasassayed using a conventional 4 hour Indium-111 release assay usingnormal human PBMC as effector cells, and the results are shown as thepercent isotope release (% lysis) in Table 2 (ADCC data).

TABLE 2 ADCC activity of NPC-1 with various tumor cell lines. % SpecificKilling (±SD) Effector:Target Tumor Cell Line Cell Ratio No mAb NPC-1LS174T Colorectal   50:1 3.2 ± 0.4 18.8 ± 0.5   25:1 2.4 ± 0.1 16.2 ±1.9 12.5:1 1.4 ± 0.7 15.1 ± 3.3 CFPAC-1 Pancreatic   50:1 1.9 ± 0.8 10.1± 1.2   25:1 −0.6 ± 1.0 8.1 ± 0.9 12.5:1 −1.1 ± 0.4 3.8 ± 0.9 OVCAR-3Ovarian  100:1 2.4 ± 0.4 −1.5 ± 0.7   50:1 −0.1 ± 0.8 −0.8 ± 1.0   25:10.5 ± 0.5 0.0 ± 0.3 12.5:1 0.4 ± 0.5 −0.4 ± 0.1Antibody-dependent cell cytotoxicity assay with various tumor celllines. Assay was performed with 5 μg NPC-1 antibody per well.

Example 7. SDS Polyacrylamide Gel Electrophoresis Analysis of NPC-1

The native configuration of murine immunoglobulin gamma (IgG1) iscomprised of four polypeptides, with two polypeptides each of a heavychain and a light chain. One heavy chain (55 kilodaltons) is associatedwith one light chain (25-29 kilodaltons) and this dimer is linked to anidentical dimer through disulfide bonding to complete the functionaltetrameric macromolecule. The IgG molecule can be dissociated into itscomponent heavy and light chains and separated by size on polyacrylamidegel matrix in the presence of denaturing reagent (SDS, sodium dodecylsulfate) and an agent to reduce the disulfide bridge that links the twoheterodimers (DTT, dithiothreitol). Gel electrophoresis is a commonanalytical method used to define the molecular mass of proteinaceousmaterials, such as antibodies.

Purified NPC-1 was subjected to analysis by SDS polyacrylamide gelelectrophoresis in the presence of reducing agent (DTT). Threemicrograms of purified NPC-1 was mixed with DTT and 4× samples buffercontaining SDS, glycerol, and bromophenol blue dye. The mixture washeated to 95° C. for 2 minutes, cooled on ice, then loaded onto an SDSgradient polyacrylamide gel (4%-20% gradient) and subjected to anelectric current to separate the molecular species in the NPC-1preparation. Following electrophoresis, the gel was stained withCoomassie Blue dye to visualize the proteins on the gel, destained withwater, and dried between porous plastic sheets. The data (not shown)revealed two protein bands of molecular mass 55 kilodaltons,representing the heavy chain, and 28 kilodaltons, representing the lightchain molecular species, respectively. These data show that the purifiedmaterial correspond to the known molecular sizes for murine IgG1.

Example 8. Pre-Clinical Anti-Tumor Efficacy Study Design UsingChimerized NPC-1 (NPC-1Chi) Antibody

Athymic nude mice, aged 4-6 month old, are used in this study. LS174Tcolorectal tumor cells and AsPC-1 human pancreatic tumor cells are usedas the tumor models. The tumors are established by implanting 2e6 tumorcells subcutaneously on the flank of mice. Solid tumors grow toapproximately 200 mm3 in 10-14 days, at which time the mice are recagedand randomized into study groups of 10 (n=10). Mice are injectedintraperitoneally with NPC-1Chi and human effector cells (PBMC) every 3days for a total of 3 cycles of injections. The mice are inspected dailyfor general health, and the tumors are measured with a digital calipertwice a week for approximately 28-40 days. Control mice with tumorvolumes greater than 2000 mm3 are sacrificed by CO2 inhalation orcervical dislocation according to local IACUC guidelines. Tumor growthis plotted and statistical analysis is performed using ANOVA.

Experimental Groups:

Group Number Tumor Antibody Dose (ug) Effector Cells 1 10 LS174T HumanIgG 400 None 2 10 LS174T Human IgG 400 Human PBMC 3 10 LS174T NPC-1Chi400 None 4 10 LS174T NPC-1Chi 400 Human PBMC 5 10 AsPC-1 Human IgG 400None 6 10 AsPC-1 Human IgG 400 Human PBMC 7 10 AsPC-1 NPC-1Chi 400 None8 10 AsPC-1 NPC-1Chi 400 Human PBMC

Example 9. Pre-Clinical Pharmacology-Toxicity Study Design UsingChimerized NPC-1Chi (NPC-1Chi) Antibody

Two mouse strains are used in this study. The first is the athymic nudemouse bearing the subcutaneous AsPC-1 pancreatic tumor to study the drugmetabolism-pharmacokinetics (DMPK) in a tumor-bearing animal and tostudy the localization of the antibody at the tumor site. The secondmodel is the non-tumor-bearing normal mouse to study DMPK reactions inan immunocompetent animal. Four- to six-month old mice are used in thestudy. AsPC-1 pancreatic tumors are established by implanting 2e6 tumorcells subcutaneously on the flank of mice. Solid tumors grow toapproximately 200 mm3 in 10-14 days, at which time mice are recaged andrandomized into study groups of 8 (n=4 per group per timepoint). Onstudy day-one, mice are bled for pre-treatment analysis of blood andserum. On study day one, all mice are injected intraperitoneally withNPC-1Chi or control IgG. In addition, tumor-bearing nude mice areinjected intraperitoneally with human effector cells or saline. On studyday four (72 hours post-injection), four mice per group are sacrificedfor DMPK analysis. On study day eleven, the remaining four mice pergroup are sacrificed for DMPK analysis. The DMPK analysis includeshematology (complete blood cell count/differential), serum analysis(AST, ALT, BILI, CPK, CK, CREAT, CBA bead analysis for lymphokines),histological analysis (H&E stain of liver, spleen, pancreas, lung,kidney), and immunohistochemical analysis of NPC-1 localization andquantitation. Values are analyzed statistically among groups by t-test.

Experimental Groups:

Dose Group Mice Day Mouse Tumor Antibody (ug) Effector Cells 1 4 4 NudeLS174T Human IgG 400 None 2 4 4 Nude LS174T Human IgG 400 Human PBMC 3 44 Nude LS174T NPC-1Chi 400 None 4 4 4 Nude LS174T NPC-1Chi 400 HumanPBMC 5 4 4 BALB/c Human IgG 400 None 6 4 4 BALB/c Human IgG 400 HumanPBMC 7 4 4 BALB/c NPC-1Chi 400 None 8 4 4 BALB/c NPC-1Chi 400 Human PBMC9 4 11 Nude LS174T Human IgG 400 None 10 4 11 Nude LS174T Human IgG 400Human PBMC 11 4 11 Nude LS174T NPC-1Chi 400 None 12 4 11 Nude LS174TNPC-1Chi 400 Human PBMC 13 4 11 BALB/c Human IgG 400 None 14 4 11 BALB/cHuman IgG 400 Human PBMC 15 4 11 BALB/c NPC-1Chi 400 None 16 4 11 BALB/cNPC-1Chi 400 Human PBMC

Example 10. Phase I Study of NPC-1

This trial with a chimeric version of mAb NPC-1 examines 3 dose levels(10 mg/M², 25 mg/M² and 50 mg/M² per week) given in cycles of 4 weeklydoses. Any significant bowel toxicity is documented. All patients aremonitored for blood in stool. Colonoscopy is used to investigate anybleeding, and random biopsy of the patients' colon mucosae may determinespecific abnormalities.

Treatment continues for six months. Anticancer activity is monitored atall three dose levels. CPAA serum levels are monitored, and CT analysismay reveal a partial response of colon, pancreatic, lung, liver andlymph node metastases. Patient stability is monitored for one year.

Example 11. Chimerization of the Murine NPC-1 Antibody (NPC-1C)

When monoclonal antibodies are used as therapeutic agents to treatcancer patients, it is often beneficial to re-engineer the murineantibody to reduce its immunogenicity in humans: the administration of100% murine antibodies in humans has been shown to elicit humananti-mouse antibody responses (HAMA), which severely reduce thetherapeutic value of the antibody and may induce toxicity. Lessimmunogenic antibodies intended for use in humans may be made byreplacing the majority of the murine immunoglobulin sequence with humanimmunoglobulin sequences, as described above. Such replacementsdramatically reduce the immunogenicity and toxicity of the therapeuticagent intended for use in humans. Chimerization is one method forreducing the immunogenicity of murine antibodies and is the mostconservative approach with respect to preserving the antigen recognitionspecificity. In the chimerization process, approximately 66% of themurine immunoglobulin sequence is replaced with human immunoglobulinframework sequences. One can select the human immunoglobulin isotype(IgG1, IgG2, etc.) with specific known activities depending on theintended use and mechanism of action of the resulting antibody. Inaddition, one can perform less conservative steps to graft simply themurine CDR loops onto the framework of a human immunoglobulin framework.This process is known as “CDR grafting” or “humanization”. This processresults in antibodies that are 90% to 95% human protein. Alternatively,one can “fully humanize” a murine antibody by even less conservativemethods such as lambda phage display or specific amino acid replacementin the CDR loops of a human antibody to result in an altered antigenbinding specificity.

Another benefit of re-engineering the murine antibody to be produced ina recombinant expression system is that the genes coding for the heavyand light chain molecules comprising the fully assembled antibody can bealtered at this stage. One may make changes in codon usage to enhanceprotein expression levels in the species of cell that will be used toproduce the antibodies. For example, it is known that there aredifferences in percent codons used for specific amino acids in hamstercells compared to human cells. Alternatively, one can introducealternative amino acids that would result in an antibody that hasdifferent carbohydrate processing in the producer cells. Such differentcarbohydrate composition can alter the activities of the antibodyproduct. In addition, the introduction of alternative amino acids in theconstant regions of the antibody, or the use of different humanimmunoglobulin isotypes, can alter the biological activities of thefinal antibody product. For example, one can change the mechanism ofcytotoxicity of an antibody from primarily cell-mediated cytotoxicity(ADCC) to primarily complement-mediated cytotoxicity (CDC). Thisrepresents a partial list of alterations that may be made to an antibodyto enhance specific functions or expression of an antibody intended foruse in humans.

The NPC-1C chimeric antibody was designed to include the variableregions of the heavy and light chains of murine NPC-1 linked to thehuman immunoglobulin gamma-1 and kappa constant regions, respectively. Amammalian expression vector containing the murine dihydrofolatereductase (dhfr) gene (Biofactura, Rockville, Md.) utilizes the hCMVpromoter/enhancer region to efficiently transcribe the light and heavychain genes and the dhfr gene as a selectable marker (pBF-dhfr). Thisvector provides a high level of antibody production in Chinese HamsterOvary (CHO) cells. The genes encoding the murine sequence for NPC-1heavy and light chains linked to the human constant regions werechemically synthesized using codon sequences optimized for CHO cells andcontaining the correct restriction enzyme sites at the 5′ and 3′ endsfor simple and direct cloning into the pBF-dhfr mammalian expressionvector. The genes were provided in pUC shuttle plasmids followingsequence verification.

A two-step process was used to construct the dual gene vector containingboth the heavy and light chain genes encoding NPC-1. Each chain wascloned separately into the pBF-dhfr vector. The NPC-1 chi heavy chainwas ligated into the KpnI site of the pBF-dhfr vector, generating Clone19 in the appropriate reading frame. NPC-1chi LC containing BglII endswas ligated into the BamHI site of pBF-dhfr vector generating clone 1 inthe appropriate reading frame. Clone 1 DNA was used to PCR amplify anNPC-1 LC cassette containing BglII ends and the hCMV promoter and NPC-1chi LC. The following primers were utilized for the amplification ofNPC-1chi LC cassette containing BglII ends: 5′ CMV cassette primer:5′GTC ACT AGA TCT GCC GTT GAC ATT GAT TAT TGA C 3′ (SEQ ID NO:13) and 3′BGHpA cassette primer: 5′ ACA CTG AGA TCT TCC CCA GCA TGC CTG CTA TTGTCT T 3′ (SEQ ID NO:14) using Invitrogen's AccuPrime Pfx DNA polymeraseaccording to manufacturer's instructions. Briefly, the template, 200 ngof Clone 1 DNA was denatured for 2 min. at 95° C. (Hot Start), followedby thirty cycles of 94° C. for 15 sec., 55° C. for 30 sec., and 68° C.for 2 min. The PCR product was analyzed and cut out of a 1% Agarose TAEgel, eluted with a QIAquick gel elution system (Qiagen) and the ends cutwith BglII.

The gel purified fragment was ligated into BglII cut clone 19 containingthe heavy chain. Chemically competent DH5alpha E. coli cells weretransformed with the ligated DNA and colonies screened with NdeI. Cloneswith a small NdeI fragment (0.75 kb) contained a construct with opposingLC and HC cassettes. A large NdeI fragment (1.9 kb) contained aconstruct with LC and HC cassettes in tandem. Six clones of each typewere used to transfect human 293T cells with Lipofectamine-2000(Invitrogen).

Example 12. Expression and Purification of NPC-1C

The chimerized antibody NPC-1C was cloned into a mammalian expressionplasmid DNA designated pBF-dhfr. The resulting DNA was namedNPC-1C-pBF-dhfr. Two clones were selected, 13-0 (opposing orientation)and 9T (tandem orientation) for the development of an antibody producingstable CHO cell line. The plasmids were grown in LB-ampicillin (1 liter)and purified by CsCl ultracentrifugation (2×) and transfected intoCHO-DG44 cells using Lipofectamine 2000 (Invitrogen). Stable NPC-1Cexpressing CHO cell lines were developed by an amplification procedureby increasing the Methotrexate concentrations. Clones expressing highlevels of functional antibody were selected and grown.

The NPC-1C antibody was purified from culture medium followingtransfection of either CHO cells or 293T cells. The antibody was usedfor characterization the biological functions of the chimeric antibody.Cell culture medium was collected following 4 days of incubation fromthe time of transfection with the expression plasmid. The medium wasdiluted with 10×PBS to yield a final 1× concentration of PBS to adjustthe salt concentration and pH of the medium for efficient binding toprotein A. The medium was applied to a protein A-Sepharose resin in aglass column. The resin was washed extensively with PBS, then the boundantibody was eluted with 0.1M glycine pH 3.0 and the fractionscontaining the protein peak were pooled and dialyzed extensively againstPBS pH 7.4. The purified chimeric antibody was stored at 4o for latercharacterization and testing.

The purified NPC-1C antibody was characterized by standard gelelectrophoresis on a 4% to 20% gradient SDS-polyacrylamide gel. Theantibody was run under both non-reducing and reducing conditions toevaluate the amount of intact, fully assembled tetrameric antibody (150kD, representing H₂L₂) versus the amount of heavy chain (50 kD) andlight chain (25 kD) proteins expressed in the recombinant expressionsystem from the NPC-1C-pBF-dhfr plasmid.

Example 13. Tumor Cell Binding Specificity of NPC-1C

The chimeric NPC-1C mAb produced by transient transfection of 293T cellswas purified by affinity chromatography using protein A-Sepharosematrix. The purified NPC-1C was characterized by indirectimmunofluorescence, using various tumor cells listed in Table 3 below.All of the tumor cell lines were obtained from the ATCC. Cells wereincubated with purified NPC-1C diluted in phosphate buffered saline(PBS) for 1 hour at 4° C. The cells were washed and incubated with afluorescein-labelled goat anti-human immunoglobulin antibody. The cellswere then washed with PBS and examined by flow cytometry using aBecton-Dickinson FACScalibur and CellQuest analysis software. Theresults appear in Table 3 (FACS data). The data demonstrate theselective binding of NPC-1C to some colorectal and pancreatic tumor celllines, but not to squamous or prostate tumor cell lines. It should benoted that the data in Table 3 were generated with approximately 16-foldlower.antibody concentration than is typically tested in this assayformat. Thus, the percent of calls that stained positively and theintensity of the staining (mean fluorescence intensity, mfi) arereported here using a sub-optimal amount of the NPC-1C antibody whichmay under-report the actual cell binding potential of the antibody in atypical cell binding experiments using an optimized antibodyconcentration.

TABLE 3 Cell binding activity of NPC-1C antibody % Cell Staining (mfi)NPC-1Chi NPC-1Chi Tumor Cell Line FITC-Ab only (prep 1) (prep 2) LS174TColorectal 1.26 (19) 11.59 (43) 11.22 (47) SW480 Colorectal 0.69 (26)1.41 (44) 1.34 (64) SW620 Colorectal 0.52 (101) 0.24 (184) 0.85 (74)SW1463 Colorectal 0.95 (37) 3.72 (410) 4.29 (399) SW1116 Colorectal 1.13(54) 1.12 (97) 2.37 (174) HT-29 Colorectal 1.14 (63) 1.30 (55) 1.09 (34)Colo-205 Colorectal 0.65 (28) 2.26 (154) 1.44 (67) CFPAC-1 Pancreatic1.20 (17) 11.23 (16) 10.55 (15) AsPC-1 Pancreatic 0.04 (29) 0.43 (33)0.35 (34) Panc-1 Pancreatic 1.04 (14) 0.75 (69) 0.41 (31) H520 Squamous1.48 (64) 1.66 (129) 0.93 (173) H226 Squamous 1.39 (38) 0.49 (32) 0.40(32) HTB-35 Squamous 3.96 (37) 4.83 (97) 3.85 (123) SW756 Squamous 1.63(117) 0.75 (186) 2.14 (178) PC-3 Prostate 1.49 (11) 1.34 (17) 1.52 (28)DU14 Prostate 0.41 (69) 0.24 (17) 0.14 (277)Flow cytometric antibody binding data with various cultured tumor celllines. Cells stained with 2 μg NPC-1C per 100,000 cells.

Example 14. ADCC Activity of NPC-1C Demonstrating Anti-TumorCytotoxicity

A therapeutically useful mAb, specific for an immunogenic tumor antigen,should have one or more of the following properties: (a) high tumortissue specificity, (b) absence of cross-reactivity to normal humantissue, and (c) a biological activity associated with destruction oftumors, such as antibody-dependent cellular cytotoxicity (ADCC). TheADCC activity of NPC-1C was tested on colon and pancreatic carcinomalines as target cells. Melanoma and prostate tumor cell lines wereincluded as a specificity controls. ADCC was assayed using aconventional four-hour ¹¹¹Indium release assay using normal activatedhuman PBMC as effector cells, and the results are shown as the percentspecific isotope release (% lysis) in Table 4 (ADCC data). The datademonstrate robust in vitro killing of colorectal and pancreatic tumorcell lines mediated specifically by the NPC-1C antibody. In contrast, nocytotoxicity was measured against the melanoma or prostate tumor linecontrols tested in the assay, demonstrating specific NPC-1C-dependentrecognition and killing of colorectal and pancreatic tumor cells. Itshould be noted that the data in Table 4 were generated withapproximately 16-fold lower antibody concentration than is typicallytested in this assay format. Although robust and specific cytotoxicitywas observed using a sub-optimal concentration of NPC-1C, these data mayunder-report the actual cytotoxic potential of the antibody in a typicalADCC experiment using an optimized antibody concentration.

TABLE 4 ADCC activity of NPC-1C antibody. % Specific Killing (±SEM)Effector:Target Isotype control Tumor Cell Line Cell Ratio Ab NPC-1CColo-205 (Colorectal)   50:1 9.8 ± 1.9 66.7 ± 0.6   25:1 0.8 ± 1.2 46.4± 1.6 12.5:1 −0.5 ± 0.1 32.8 ± 2.0 SW620 (Colorectal)   50:1 1.6 ± 0.263.7 ± 2.9   25:1 3.5 ± 1.8 61.0 ± 1.8 12.5:1 0.0 ± 0.3 51.5 ± 0.9SW1463 (Colorectal)   50:1 0.1 ± 1.1 33.8 ± 1.0   25:1 −1.3 ± 0.2 25.5 ±0.6 12.5:1 −1.2 ± 0.1 17.9 ± 1.7 LS174T (Colorectal)   50:1 −1.2 ± 0.126.8 ± 2.9   25:1 −0.8 ± 0.1 18.5 ± 4.1 12.5:1 −1.1 ± 0.0 9.5 ± 0.5AsPC-1 (Pancreatic)   50:1 −0.8 ± 2.9 44.5 ± 6.8   25:1 −7.0 ± 2.2 36.2± 2.6 12.5:1 −1.2 ± 0.9 26.5 ± 6.7 CFPAC-1 (Pancreatic)   50:1 −1.2 ±2.3 26.9 ± 1.6   25:1 −2.4 ± 0.1 23.2 ± 2.2 12.5:1 −2.0 ± 0.4 11.1 ± 1.6PANC-1 (Pancreatic)   50:1 −2.2 ± 0.4 46.8 ± 2.1   25:1 −2.5 ± 0.4 33.2± 3.3 12.5:1 −3.9 ± 0.3 21.2 ± 0.6 SK-MEL (Melanoma)   50:1 2.7 ± 0.74.6 ± 1.1   25:1 1.5 ± 0.3 3.3 ± 1.1 12.5:1 1.6 ± 0.4 2.3 ± 0.6 DU145(Prostate)   50:1 −0.3 ± 0.2 −0.5 ± 0.3   25:1 −0.7 ± 0.1 0.3 ± 0.812.5:1 −0.2 ± 0.2 −0.3 ± 0.1Antibody-dependent cell cytotoxicity assay with various tumor celllines. Assay was performed with 250 ng NPC-1C per well.

Example 15. Immunohistochemical Staining of Human Tissues by NPC-1CDemonstrating Specific Cancer Cell Binding

The NPC-1C antibody was tested for its ability to specifically stain anumber of human tissues to demonstrate its utility as a cancerdiagnostic and monitoring antibody. These tissues were tested as bothcollections of microarrays containing multiple samples, and asindividual biopsy tissue sections, both frozen and in paraffin blocks.Immunohistochemical staining can reveal the applicability of theantibody as a useful research or commercial product.

The purified NPC-1C antibody was first biotinylated using a commercialkit (Roche) to control for background staining that is known to occurwhen using a human antibody to stain human tissues. The biotinylatedNPC-1C antibody was tested at 5 μg/mL diluted in PBS buffer againsttissue sections and tissue arrays slides from Accurate Chemical Co.(Westbury, N.Y.). Paraffin tissues were first de-paraffinized. Frozentissues were thawed and washed in PBS. Paraffin tissues were incubatedwith Peroxo Block (Zymed, San Francisco, Calif.) for 1.5 min. Frozentissues were incubated with Peroxo Block (Zymed) for 30 sec. Bothsamples were rinsed 3× in PBS, then incubated with avidin for 10 min.(Zymed), and rinsed 3× with PBS. Samples were then incubated with CASBlock for 10 min. (Zymed) and shaken off the sample (no washing). TheNPC-1C was incubated with the tissues for 1 hour, then rinsed off 3×with PBS. Streptavidin/HRP (Dako, Carpinteria, Calif.) was applied at a1:400 dilution for 30 min., then washed 3× with PBS. The DAB substrate(Zymed) was added for 1 min, then washed 3× with PBS. Samples were thencounterstained with hematoxylin for 3 min then rinsed and mounted onglass slides for analysis under a light microscope. Samples were scoredfor the number and intensity of immunostaining specifically with theNPC-1C antibody. Samples were scored with a 0-1-2-3 system whichreflects both the number of cells that stain positive in the section andthe intensity of the brown stain per cell.

The samples tested were tissues independently diagnosed by a pathologistas colon cancer, normal colon, pancreatic cancer, normal pancreas, orcancer of the uterus or prostate. The data from the immunohistochemicalstaining with NPC-1C is shown in Table 5 below. The data demonstratethat the NPC-1C antibody stains tissues from both colon cancers (43% ofall samples tested, n=48) and pancreatic cancers (32% of all samples,n=11), whereas NPC-1C does not cross-react with normal pancreas andcross-reacted with only 25% of normal colon tissues tested. When NPC-1Cwas tested for staining against other cancer types, it showed someimmunoreactivity with an antigen expressed on uterine cancer samples(24%, n=42) but not normal uterus tissue, and 24% of prostate cancersamples (n=40) but not with normal prostate samples. The data show aselective binding specificity of NPC-1C for colon and pancreatic cancertissues, with some reactivity to uterine and prostate cancer tissues.There was no cross-reactivity, however, of NPC-1C with normal tissuesfrom pancreas, uterus or prostate, and a minor fraction of normal colontissues.

TABLE 5 Immunohistochemical staining of human tissue samples with NPC-1CHuman Tissue staining intensity tissue sample Negative Weak +1 +2 +3 +4Colon cancer 27/48 5/48 7/48 4/48 5/48 (Accumax array)  (56%) (10%)(15%)  (8%) (10%) Normal colon 3/4 1/4  (Accumax array)  (75%) (25%)Pancreas cancer  7/11 4/11 (CHTN)  (64%) (32%) Normal pancreas 3/3(CHTN) (100%) Uterus cancer 32/42 2/42 8/42 (Accumax array)  (76%)  (5%)(19%) Normal uterus 12/12 (Accumax array) (100%) Prostate cancer 30/405/40 5/40 (Accumax array)  (75%) (12%) (12%) Normal prostate 4/4(Accumax array) (100%)

Having now fully described this invention, it will be appreciated bythose skilled in the art that the same can be performed within a widerange of equivalent parameters, concentrations, and conditions withoutdeparting from the spirit and scope of the invention and without undueexperimentation.

Although this invention has been described in connection with specificembodiments thereof, it will be understood that it is capable of furthermodifications. This application is intended to cover any variations,uses, or adaptations of the inventions following, in general, theprinciples of the invention and including such departures from thepresent disclosure as come within known or customary practice within theart to which the invention pertains and as may be applied to theessential features hereinbefore set forth as follows in the scope of theappended claims.

1-14. (canceled)
 15. An isolated nucleic acid encoding at least one ofthe light or heavy chain of an a monoclonal antibody or antigen-bindingfragment thereof that binds to a human colorectal and pancreaticcarcinoma-associated antigen (CPAA), wherein said antibody comprises thelight chain CDR1 amino acid sequence of SEQ ID NO:7, light chain CDR2amino acid sequence of SEQ ID NO:8, and light chain CDR3 amino acidsequence of SEQ ID NO:9, and wherein said monoclonal antibody orantigen-binding region thereof comprises the heavy chain CDR1 amino acidsequence of SEQ ID NO:10, heavy chain CDR2 amino acid sequence of SEQ IDNO:11, and heavy chain CDR3 amino acid sequence of SEQ ID NO:12.
 16. Theisolated nucleic acid of claim 15, which comprises SEQ ID NO: 1 or SEQID NO:
 2. 17. The isolated nucleic acid of claim 15, which comprises anucleic acid that encodes the sequence encoded by SEQ ID NO: 1 or SEQ IDNO:
 2. 18. The isolated nucleic acid of claim 15, which comprises anucleic acid that encodes the amino acid sequence of SEQ ID NO:
 3. 19.The isolated nucleic acid of claim 15, which comprises SEQ ID NO: 4 orSEQ ID NO:
 5. 20. The isolated nucleic acid of claim 15, which encodesthe sequence encoded by SEQ ID NO: 4 or SEQ ID NO:
 5. 21. The isolatednucleic acid of claim 15, which comprises a nucleic acid that encodesthe amino acid sequence of SEQ ID NO:
 6. 22. The isolated nucleic acidof claim 15, wherein the light chain of said antibody comprises theamino acid sequence of SEQ ID NO: 3 and the heavy chain of said antibodycomprises the amino acid sequence of SEQ ID NO:
 6. 23. The isolatednucleic acid of claim 15, wherein the light chain of said antibodycomprises the amino acid sequence encoded by SEQ ID NO: 1 or SEQ ID NO:2 and the heavy chain of said antibody comprises the amino acid sequenceencoded by SEQ ID NO: 4 or SEQ ID NO:
 5. 24. The isolated nucleic acidof claim 15, wherein said antibody is a chimeric, humanized, orbifunctional antibody, or an antigen-binding fragment thereof.
 25. Theisolated nucleic acid of claim 15, wherein said antibody comprises ahumanized heavy chain and comprises a humanized light chain.
 26. Theisolated nucleic acid of claim 15, wherein said antibody comprises aFab, Fab′, F(ab′)2, Fv, or a portion of the antibody that is capable ofbinding said antigen.
 27. The isolated nucleic acid of claim 15, whereinsaid antibody is a chimeric antibody comprising human immunoglobulingamma-1 and kappa constant regions.
 28. The isolated nucleic acid ofclaim 15, wherein said antibody comprises a human IgA, IgM, or IgAconstant region.
 27. The isolated nucleic acid of claim 15, wherein saidantibody comprises a human IgG1, IgG2, IgG3, or IgG4 constant region.30. The isolated nucleic acid of claim 15, wherein said CPAA is anantigen bound by an NPC-1 monoclonal antibody.
 31. An isolated vectorcomprising the isolated nucleic acid of claim
 15. 32. An isolated cellcomprising the isolated nucleic acid of claim
 15. 33. An isolated cellcomprising the vector of claim
 31. 34. A method of producing at leastone of the light chain or heavy chain of an anti-CPAA antibody or anantigen-binding fragment thereof, comprising expressing the isolatednucleic acid of claim 15.